Package 'rbioapi'

Description

Run this function to test the internet connectivity of your device and the current status of the supported Services.

Usage

rba_connection_test(print_output = TRUE, diagnostics = FALSE)

Arguments

Details

This function attempts to send a simple query to the supported services. If the service successfully responded, you will be informed with a success message; If not, the content of the error will be reported to you.
Please run this function if you encounter any errors while using rbioapi. Also, if you need to contact support, kindly call this function with 'diagnostic = TRUE' and include the output messages in your support request.

Value

Connection test for the supported servers will be displayed in console and the results will be invisibly returned as a list.

See Also

Other "Helper functions": rba_options(), rba_pages()

Examples

rba_connection_test()

Description

This function provides a convenient one-step wrapper for performing enrichment analysis on a given gene list using Enrichr. It simplifies the process by internally calling the necessary functions in the correct order. See the details section for more information.

Usage

rba_enrichr(
  gene_list,
  description = NULL,
  gene_set_library = "all",
  regex_library_name = TRUE,
  organism = "human",
  background_genes = NULL,
  progress_bar = TRUE,
  ...
)

Arguments

Details

This function will call other rba_enrichr_*** functions with the following order:

1. (If necessary) Call rba_enrichr_libs to obtain a list of available libraries in Enrichr for the given organism.

2. Call rba_enrichr_add_list to upload your gene-list and obtain a 'user list ID'.

3. (If necessary) Call rba_enrichr_add_background to upload your background gene-list and obtain a 'background list ID'.

4. Call rba_enrichr_enrich to perform enrichment analysis on the gene-list against one or multiple Enrichr libraries

Value

A list containing data frames of the enrichment results of your supplied gene-list against the selected Enrichr libraries.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/datasetStatistics"
"POST https://maayanlab.cloud/Enrichr/addList"
"POST https://maayanlab.cloud/speedrichr/api/addList"
"POST https://maayanlab.cloud/speedrichr/api/addbackground"
"GET https://maayanlab.cloud/Enrichr/enrich"
"POST https://maayanlab.cloud/speedrichr/api/backgroundenrich"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

Other "Enrichr": rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Other "Enrichment/Over-representation": rba_mieaa_enrich(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment(), rba_string_enrichment_image()

Examples

## Not run: 
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"))

## End(Not run)

rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)


rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "go",
    regex_library_name = TRUE)

Description

In addition to the main gene list, you can also submit a background gene list to Enrichr. This gene list can be used later to compute the statistics of the enrichment analysis.

Usage

rba_enrichr_add_background(background_genes, ...)

Arguments

Details

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

Value

A list with the unique IDs for your uploaded background gene list.

Corresponding API Resources

"POST https://maayanlab.cloud/speedrichr/api/addbackground"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

my_background_genes <- c(
"NSUN3", "POLRMT", "NLRX1", "SFXN5", "ZC3H12C", "SLC25A39", "ARSG",
"DEFB29", "PCMTD2", "ACAA1A", "LRRC1", "2810432D09RIK", "SEPHS2",
"SAC3D1", "TMLHE", "LOC623451", "TSR2", "PLEKHA7", "GYS2", "ARHGEF12",
"HIBCH", "LYRM2", "ZBTB44", "ENTPD5", "RAB11FIP2", "LIPT1",
"INTU", "ANXA13", "KLF12", "SAT2", "GAL3ST2", "VAMP8", "FKBPL",
"AQP11", "TRAP1", "PMPCB", "TM7SF3", "RBM39", "BRI3", "KDR", "ZFP748",
"NAP1L1", "DHRS1", "LRRC56", "WDR20A", "STXBP2", "KLF1", "UFC1",
"CCDC16", "9230114K14RIK", "RWDD3", "2610528K11RIK")

rba_enrichr_add_background(background_genes = my_background_genes)

Description

This function uploads your gene list to Enrichr and retrieves a unique 'user list ID' required for performing enrichment analysis.

Usage

rba_enrichr_add_list(
  gene_list,
  description = NULL,
  organism = "human",
  speedrichr = FALSE,
  ...
)

Arguments

Details

Enrichr uses separate APIs for analysis with or without a background gene list. Set 'speedrichr = TRUE' if this gene list will be used with a background gene list; otherwise, set it to FALSE. Gene lists submitted with 'speedrichr = TRUE' can only be analyzed with a background set, and those submitted with 'speedrichr = FALSE' can only be analyzed without one. Currently, background-based enrichment is supported only for human libraries.

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

Value

A list with the unique IDs for your uploaded gene list. 'userListId' is the ID required for later steps.

Corresponding API Resources

"POST https://maayanlab.cloud/Enrichr/addList"
"POST https://maayanlab.cloud/speedrichr/api/addList"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

rba_enrichr_add_list(gene_list = c("TP53", "TNF", "EGFR"),
     description = "tumoral genes",
     speedrichr = FALSE)


rba_enrichr_add_list(gene_list = c("RAG1", "RAG2", "DNTT", "LIG4", "ARTEMIS"),
     description = "TCR rearrangment",
     speedrichr = TRUE)

Description

This function retrieves enrichment analysis results for your supplied 'user_list_id' against one or multiple Enrichr libraries.

Usage

rba_enrichr_enrich(
  user_list_id,
  gene_set_library = "all",
  regex_library_name = TRUE,
  organism = "human",
  background_id = NULL,
  progress_bar = TRUE,
  ...
)

Arguments

Details

If 'background_id' is supplied, this function will interact with the speedrichr API. In this case, 'user_list_id' must have been obtained from a rba_enrichr_add_list call with the 'speedrichr' parameter set to 'TRUE'. Additionally, this feature is only available for "human" organism.

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

Value

A list containing data frames of the enrichment results of your supplied gene-list against the selected Enrichr libraries.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/enrich"
"POST https://maayanlab.cloud/speedrichr/api/backgroundenrich"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

## Not run: 
rba_enrichr_enrich(user_list_id = 11111)

## End(Not run)
## Not run: 
rba_enrichr_enrich(user_list_id = 11111,
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)

## End(Not run)
## Not run: 
rba_enrichr_enrich(user_list_id = 11111,
    gene_set_library = "go",
    regex_library_name = TRUE)

## End(Not run)

Description

This function will search the gene and retrieve a list of Enrichr Terms that contains that gene.

Usage

rba_enrichr_gene_map(gene, categorize = FALSE, organism = "human", ...)

Arguments

Value

A nested list containing the search results of your supplied gene.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/genemap"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

rba_enrichr_gene_map(gene = "p53")


rba_enrichr_gene_map(gene = "p53", categorize = TRUE)

Description

This function retrieves a list of libraries available in Enrichr along with their associated statistics. Each library represents a collection of gene sets that can be used for enrichment analysis.

Usage

rba_enrichr_libs(organism = "human", store_in_options = TRUE, ...)

Arguments

Details

By default, this function will save the library names as a global option ("rba_enrichr_libs") for other Enrichr functions that internally require the names of Enrichr libraries. You should call this function once per R session with the argument 'store_in_options = TRUE' before using rba_enrichr_enrich or rba_enrichr. However, if you do not explicitly call it, rbioapi will automatically execute this function in the background the when it is needed.

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

Value

A data frame with the names of available library in Enrichr and their statistics.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/datasetStatistics"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_view_list()

Examples

rba_enrichr_libs()

Description

Retrieve the list of uploaded genes with a given 'user list ID'.

Usage

rba_enrichr_view_list(
  user_list_id,
  organism = "human",
  speedrichr = FALSE,
  ...
)

Arguments

Value

A list containing the genes and description associated to the supplied user_list_id.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/view"

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs()

Examples

## Not run: 
rba_enrichr_view_list(user_list_id = 11111)

## End(Not run)

Description

JASPAR organizes matrix profiles into collections. Using this function, you can retrieve a list of available collections in a JASPAR release.

Usage

rba_jaspar_collections(release = 2024, ...)

Arguments

Value

A data frame with collections' names and URLs.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/collections/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_collections(release = 2024)

Description

Using this function you can list all matrix profiles that are available in a collection from a JASPAR release.

Usage

rba_jaspar_collections_matrices(
  collection,
  release = 2024,
  only_last_version = FALSE,
  search = NULL,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

Details

The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Value

A list that contains a data frame with information of matrix profiles available in the collection.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/collections/{collection}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_collections_matrices(collection = "CORE",
  release = 2024,
  page_size = 100,
  page = 2)

Description

Using this function you can retrieve a Position Frequency Matrices (PFM) associated with a matrix profile Identifier along with its details and annotations. If a base ID (i.e. without version suffix) was supplied, the latest version will be returned.

Usage

rba_jaspar_matrix(matrix_id, file_format = NULL, save_to = NULL, ...)

Arguments

Value

A list that contains the PFM along with its details and annotations. If file_format was supplied, an un-parsed character string with the file's content.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_matrix("MA0600.2")

## Not run: 
rba_jaspar_matrix(matrix_id = "MA0600.2",
                  file_format = "meme",
                  save_to = "my_matrix.meme")

## End(Not run)

Description

You can use this function to list the JASPAR matrix profiles that match your search query, or run the function without any arguments to return a list of every matrix profile available in the latest release.

Usage

rba_jaspar_matrix_search(
  term = NULL,
  tf_name = NULL,
  tf_class = NULL,
  tf_family = NULL,
  tax_group = NULL,
  tax_id = NULL,
  data_type = NULL,
  collection = NULL,
  release = 2024,
  only_last_version = FALSE,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.
The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Value

A list that contains a data frame of matrix profiles' information.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/api/v1/matrix/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_matrix_search(term = "FOX")
rba_jaspar_matrix_search(tf_name = "FOXP3")
rba_jaspar_matrix_search(tf_name = "FOXP3", only_last_version = TRUE)
rba_jaspar_matrix_search(tf_class = "Zipper-Type")
rba_jaspar_matrix_search(tax_group = "insects")
rba_jaspar_matrix_search(page_size = 100)

Description

Since JASPAR release 2010, the matrix profiles are versioned; So, a matrix profile Identifier has "base_id.version" naming schema. Using this function you can retrieve a list of matrix profiles associated with a base (stable) ID.

Usage

rba_jaspar_matrix_versions(base_id, order = NULL, ...)

Arguments

Value

A data frame of matrix profiles' versions information.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_matrix_versions("MA0600")

Description

If a release number was supplied, this function will return the details of that release. Otherwise, if the function was called without "release" argument, a list of all JASPAR database releases will be returned.

Usage

rba_jaspar_releases(release_number = NULL, ...)

Arguments

Value

A list that contains all JASPAR database releases' information or details of a particular release.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/releases/"
"GET https://jaspar.elixir.no/api/v1/releases/{release_number}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_releases()
rba_jaspar_releases(7)

Description

Use this function to retrieve a list of transcription factor binding sites associated with a matrix profile.

Usage

rba_jaspar_sites(matrix_id, ...)

Arguments

Value

A list that contains a data frame with binding sites information.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/sites/{matrix_id}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_sites("MA0600.1")

Description

JASPAR organizes matrix profiles from multiple species in six taxonomic groups. Use this function to retrieve a list of available species in a JASPAR database release.

Usage

rba_jaspar_species(release = 2024, search = NULL, order = NULL, ...)

Arguments

Value

A data frame with information of available species.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/species/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_species(release = 2024)

Description

JASPAR curates matrix profiles from multiple species in six taxonomic groups. Using this function you can list all matrix profiles that are available in a JASPAR release from a species.

Usage

rba_jaspar_species_matrices(
  tax_id,
  release = 2024,
  only_last_version = FALSE,
  search = NULL,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

Details

The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Value

A list that contains a data frame with information of matrix profiles available for the species.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/species/{tax_id}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_species_matrices(tax_id = 9606, page_size = 100)

Description

JASPAR organizes matrix profiles from multiple species in six taxonomic groups. Use this function to retrieve a list of available taxonomic groups in a JASPAR database release.

Usage

rba_jaspar_taxons(release = 2024, ...)

Arguments

Value

A data frame with information of available species.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/taxon/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_taxons(release = 2024)

Description

JASPAR organizes matrix profiles from multiple species in six taxonomic groups. Using this function you can list all matrix profiles that are available in a JASPAR release from a taxonomic group.

Usage

rba_jaspar_taxons_matrices(
  tax_group,
  release = 2024,
  only_last_version = FALSE,
  search = NULL,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

Details

The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Value

A list that contains a data frame with information of matrix profiles available for the taxonomic group.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/taxon/{tax_group}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_tffm(), rba_jaspar_tffm_search()

Examples

rba_jaspar_taxons_matrices(tax_group = "plants", page_size = 100)

Description

Using this function you can retrieve details and annotations of Transcription Factor flexible models (TFFMs) associated with a TFFM ID. If a base ID (i.e. without version suffix) was supplied, the latest version will be returned.

Usage

rba_jaspar_tffm(tffm_id, ...)

Arguments

Value

A list that contains the TFFM's information and annotations.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm_search()

Examples

rba_jaspar_tffm("TFFM0056.3")

Description

You can use this function to list the JASPAR TF flexible models (TFFMs) that match your search query, or run the function without any arguments to return a list of every matrix profile available in the latest release.

Usage

rba_jaspar_tffm_search(
  term = NULL,
  release = 2024,
  tax_group = NULL,
  search = NULL,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.
The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Value

A list that contains a data frame with information of query hits' TFFMs.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/api/v1/tffm/"

References

• Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059

• Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

• JASPAR API Documentation

• Citations note on JASPAR website

See Also

Other "JASPAR": rba_jaspar_collections(), rba_jaspar_collections_matrices(), rba_jaspar_matrix(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_species_matrices(), rba_jaspar_taxons(), rba_jaspar_taxons_matrices(), rba_jaspar_tffm()

Examples

rba_jaspar_tffm_search(term = "FOX")
rba_jaspar_tffm_search(tax_group = "insects")
rba_jaspar_tffm_search(page_size = 100)

Description

For each Combination of species and miRNA type, Only a pre-defined categories groups are supported. Use this function to retrieve a list of supported categories for a given combination of Species and miRNA type.

Usage

rba_mieaa_cats(mirna_type, species, ...)

Arguments

Value

a named character vector with the supported categories for your supplied input combination.

Corresponding API Resources

"GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/{species}/{mirna_type}/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Examples

rba_mieaa_cats("mature", "Homo sapiens")

Description

miRBase miRNA accession could refer to either mature or precursor miRNAs. (see: A uniform system for microRNA annotation). Use this function to mature miRNA accession to corresponding miRNA accessions or vice versa.

Usage

rba_mieaa_convert_type(
  mirna,
  input_type,
  only_unique = FALSE,
  simple_output = FALSE,
  ...
)

Arguments

Value

Depending on the arguments, a data frame or a character vectors containing the miRNA accessions in your output version.

Corresponding API Resources

"POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/mirna_precursor_converter/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_version(), rba_mieaa_enrich(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Examples

Sys.sleep(1) # to prevent 429 error during R CMD check
rba_mieaa_convert_type(mirna = c("hsa-miR-20b-5p", "hsa-miR-144-5p"),
    input_type = "mature")

Description

miEAA works with miRBASE v22 accession. Using This function you can convert a set of mature or precursor miRNA accession between two given miRBase versions.

Usage

rba_mieaa_convert_version(
  mirna,
  mirna_type,
  input_version,
  output_version,
  simple_output = FALSE,
  ...
)

Arguments

Value

Depending on the arguments, a data frame or a character vectors containing the miRNA accessions in your output version.

Corresponding API Resources

"POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/mirbase_converter/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_enrich(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Examples

Sys.sleep(1) # to prevent 429 error during R CMD check
rba_mieaa_convert_version(mirna = c("hsa-miR-20b-5p", "hsa-miR-144-5p"),
    mirna_type = "mature", input_version = 22, output_version =  16)

Description

This function is a wrapper for the multiple function calls necessary to perform enrichment analysis on a given miRNA list using miEAA. see details section for more information.

Usage

rba_mieaa_enrich(
  test_set,
  mirna_type,
  test_type,
  species,
  categories = NULL,
  p_adj_method = "fdr",
  independent_p_adj = TRUE,
  sig_level = 0.05,
  min_hits = 2,
  ref_set = NULL,
  sort_by = "p_adjusted",
  sort_asc = TRUE,
  ...
)

Arguments

Details

This function will call other rba_mieaa_*** functions with the following order:

1. Call rba_mieaa_enrich_submit to Submit an enrichment analysis request to miEAA servers, using your supplied miRNA lists and other arguments.

2. Once your job was successfully submitted, it will call rba_mieaa_enrich_status every 5 seconds, to check the status of your running server-side job and whether your analysis job is finished and the results are available.

3. Call rba_mieaa_enrich_results to retrieve the results of your enrichment analysis.

See each function's manual for more details.

Value

A data frame with your enrichment analysis results.

Corresponding API Resources

"GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Other "Enrichment/Over-representation": rba_enrichr(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment(), rba_string_enrichment_image()

Examples

## Not run: 
rba_mieaa_enrich(test_set = c("hsa-miR-20b-5p", "hsa-miR-144-5p",
 "hsa-miR-17-5p", "hsa-miR-20a-5p"),
     mirna_type = "mature",
     test_type = "ORA",
     species = 9606,
     categories = "miRPathDB_GO_Biological_process_mature")

## End(Not run)

Description

After your submitted enrichment analysis request has finished (check using rba_mieaa_enrich_status), you can retrieve the results using this function.

Usage

rba_mieaa_enrich_results(job_id, sort_by = "p_adjusted", sort_asc = TRUE, ...)

Arguments

Details

Note that using rba_mieaa_enrich is a more convenient way to automatically perform this and other required function calls to perform enrichment analysis on your input miRNA-set using miEAA.

Value

A data frame with your enrichment analysis results.

Corresponding API Resources

"GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/{job_id}"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Examples

## Not run: 
rba_mieaa_enrich_results("f52d1aef-6d3d-4d51-9020-82e68fe99012")

## End(Not run)

Description

After you have submitted your enrichment analysis (using rba_mieaa_enrich_submit) and retrieved a job-id, you can use this function to check the status of your job. Status value equal to 100 means that your requested analysis has finished and you may retrieve the results using rba_mieaa_enrich_results.

Usage

rba_mieaa_enrich_status(job_id, ...)

Arguments

Details

Note that using rba_mieaa_enrich is a more convenient way to automatically perform this and other required function calls to perform enrichment analysis on your input miRNA-set using miEAA.

Value

A list containing the status value for a analysis that corresponds to your supplied job-id.

Corresponding API Resources

"GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/{job_id}"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich(), rba_mieaa_enrich_results(), rba_mieaa_enrich_submit()

Examples

## Not run: 
Sys.sleep(1) # to prevent 429 error during R CMD check
rba_mieaa_enrich_status("f52d1aef-6d3d-4d51-9020-82e68fe99012")

## End(Not run)

Description

Using This function you can submit a request in miEAA servers to perform Over-representation or GSEA Analysis for a given set of miRNA identifiers. see "arguments" section for more information.

Usage

rba_mieaa_enrich_submit(
  test_set,
  mirna_type,
  test_type,
  species = "hsa",
  categories = NULL,
  p_adj_method = "fdr",
  independent_p_adj = TRUE,
  sig_level = 0.05,
  min_hits = 2,
  ref_set = NULL,
  ...
)

Arguments

Details

Note that using rba_mieaa_enrich is a more convenient way to automatically perform this and other required function calls to perform enrichment analysis on your input miRNA-set using miEAA.

Value

A list that contains your submitted job's ID and a URL to manually check for your job status.

Corresponding API Resources

"POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/{species}/{type}/{test}/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations note on miEAA website

See Also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status()

Examples

Sys.sleep(1) # to prevent 429 error during R CMD check
rba_mieaa_enrich_submit(test_set = c("hsa-miR-20b-5p", "hsa-miR-144-5p"),
    mirna_type = "mature",
    test_type = "GSEA",
    species = 9606,
    categories = NULL)

Description

A safe way to change rbioapi's global options and behavior. see "arguments" section for available options.
Note that you are not limited to changing the options globally, you can include the option names and values in the '...' argument of any rbioapi function to alter the option(s) only in that function call; e.g. example_function(x, diagnostics = TRUE, timeout = 300).
Alternatively, you can call this function with no arguments, i.e. rba_options(), to retrieve a data frame of available rbioapi options and their current values.

Usage

rba_options(
  diagnostics = NULL,
  dir_name = NULL,
  retry_max = NULL,
  retry_wait = NULL,
  progress = NULL,
  save_file = NULL,
  skip_error = NULL,
  timeout = NULL,
  verbose = NULL
)

Arguments

Details

Because this function validates your supplied changes, please only change rbioapi options using this function and avoid directly editing them.

Value

If called without any argument, a Data frame with available options and their information; If Called with an argument, will Return NULL but Alters that option globally.

See Also

Other "Helper functions": rba_connection_test(), rba_pages()

Examples

rba_options()
## Not run: 
rba_options(verbose = FALSE)

## End(Not run)
## Not run: 
rba_options(save_file = TRUE)

## End(Not run)
## Not run: 
rba_options(diagnostics = TRUE, progress = TRUE)

## End(Not run)

Description

Some resources return paginated results, meaning that you have to make separate calls for each page. Using this function, you can iterate over up to 100 pages. Just supply your rbioapi function and change to page argument to "pages:start_page:end_page", for example "pages:1:5".

Usage

rba_pages(input_call, ...)

Arguments

Details

To prevent flooding the server, there will be a 1 second delay between calls, also the user cannot iterate on more than 100 pages. The function will also override skip_error option and will always set it to TRUE. This means that in case of server response error (e.g. requesting pages that do not exist) an error message be returned to you instead of halting function's execution.

Value

A named list where each element corresponds to a request's page.

See Also

Other "Helper functions": rba_connection_test(), rba_options()

Examples

rba_pages(input_call = quote(rba_uniprot_taxonomy(ids = 189831,
    hierarchy = "siblings",
    page_size = 50,
    page_number = "pages:1:5")))


rba_pages(input_call = quote(rba_uniprot_taxonomy_name(name = "adenovirus",
    field = "scientific",
    search_type = "contain",
    page_size = 200,
    page_number = "pages:1:5",
    verbose = FALSE)))


rba_pages(input_call = quote(rba_panther_info(what = "families",
    families_page = "pages:9:11")))

Description

Use PANTHER services to perform over-representation enrichment analysis. You can either provide a character vector of gene IDs for over-representation analysis, or a data frame of gene IDs and expression analysis.
Please refer to the details section for more information on the statistical analysis.

Usage

rba_panther_enrich(
  genes,
  organism,
  annot_dataset,
  test_type = NULL,
  correction = "FDR",
  cutoff = NULL,
  ref_genes = NULL,
  ref_organism = NULL,
  ...
)

Arguments

Details

Over-representation Test: It assesses whether specific gene sets are represented in your input gene list differently from what is expected by chance. It uses Fisher's exact test or Binomial test to calculate p-values. Fisher's exact test determines the probability of observing the gene counts in a category based on a hypergeometric distribution; the binomial test compares the observed proportion of genes in a category to the expected proportion based on the reference list. A significant p-value indicates over-representation or under-representation of a gene set.

Statistical Enrichment Test: The statistical enrichment test uses the Mann-Whitney U (Wilcoxon Rank-Sum) test to assess if the expression values associated with genes in a specific category differ significantly from the overall distribution in the input list. This non-parametric test first ranks the numerical values and computes whether the expression values were randomly drawn from the overall distribution of values. A small p-value indicates that the numerical values for the genes in the category are significantly different from the background distribution, thus non-random patterns.

Please note that starting from rbioapi version 0.8.2, you can supply a gene expression data frame to perform statistical enrichment analysis. In earlier versions, only a character vector of gene IDs was possible, thus only over-representation analysis.

Value

A list with the parameters and results. If the analysis was successful, the results data frame are returned in the "results" element within the list. Otherwise, an error message will be returned under the "search$error" element in the returned list.

Corresponding API Resources

"POST https://www.pantherdb.org/services/oai/pantherdb/enrich/overrep"
"POST https://www.pantherdb.org/services/oai/pantherdb/enrich/statenrich"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Other "Enrichment/Over-representation": rba_enrichr(), rba_mieaa_enrich(), rba_reactome_analysis(), rba_string_enrichment(), rba_string_enrichment_image()

Examples

rba_panther_enrich(
  genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
    "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
  organism = 9606, annot_dataset = "GO:0008150",
  cutoff = 0.01
  )



expression_df <- data.frame(
  genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
    "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
  expr = runif(10, 0, 100)
  )

rba_panther_enrich(
  genes = expression_df,
  organism = 9606,
  annot_dataset = "GO:0008150"
  )

Description

Using this function, you can retrieve Orthologs, MSA or Tree topology information of a given PANTHER family.

Usage

rba_panther_family(id, what, target_organisms = NULL, ...)

Arguments

Value

For trees a list and otherwise a data frame with the requested family's information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/familyortholog"
"GET https://www.pantherdb.org/services/oai/pantherdb/familymsa"
"GET https://www.pantherdb.org/services/oai/pantherdb/treeinfo"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

rba_panther_family("PTHR10000", what = "ortholog")

Description

Using this function you can search and retrieve homolog of given gene(s).

Usage

rba_panther_homolog(genes, organism, type = "P", target_organisms = NULL, ...)

Arguments

Value

A dataframe with homologs information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/ortholog/homologOther"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

rba_panther_homolog("OR4F5", organism = 9606, type = "P")

Description

Using this function you can retrieve a list of available organisms, annotation datasets, families, and pathways which are supported in PANTHER.

Usage

rba_panther_info(what, organism_chr_loc = FALSE, families_page = 1, ...)

Arguments

Value

For families and species tree, a list and otherwise a data frame with pertinent information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/supportedgenomes"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedannotdatasets"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedpantherfamilies"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedpantherpathways"
"GET https://www.pantherdb.org/services/oai/pantherdb/speciestree"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

rba_panther_info(what = "organisms")


rba_panther_info(what = "families", families_page = 4)

Description

Using this function, you can search your genes in PANTHER database and retrieve attributes and annotations associated to your genes.

Usage

rba_panther_mapping(genes, organism, ...)

Arguments

Value

A list containing your unmapped inputs and mapped genes with pertinent information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/geneinfo"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

rba_panther_mapping(genes = c("Cd40", 7124, "ENSG00000203747", "P33681"),
    organism = 9606)

Description

Using this function you can search and retrieve orthologs of given gene(s), and optionally return the corresponding position in the target organisms' protein sequences.

Usage

rba_panther_ortholog(
  genes,
  organism,
  type = "all",
  target_organisms = NULL,
  seq_pos = NULL,
  include_msa = NULL,
  ...
)

Arguments

Value

A data frame with Orthologs information.

Corresponding API Resources

"POST https://www.pantherdb.org/services/oai/pantherdb/ortholog/matchortho"
"POST https://www.pantherdb.org/services/oai/pantherdb/ortholog/homologpos"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_tree_grafter()

Examples

rba_panther_ortholog("CD40", organism = 9606, type = "LDO")

Description

Use this function to retrieve a PANTHER family's tree topology information with a node corresponding to your sequence grafted in the best location in that tree.

Usage

rba_panther_tree_grafter(protein_seq, target_organisms = NULL, ...)

Arguments

Details

For more information, see: Haiming Tang, Robert D Finn, Paul D Thomas, TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations, Bioinformatics, Volume 35, Issue 3, February 2019, Pages 518–520, doi:10.1093/bioinformatics/bty625

Value

A list containing PANTHER tree topology information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/graftsequence"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog()

Examples

rba_panther_tree_grafter("MKVLWAALLVTFLAGCQAKVEQAVETE")

Description

Using this function, you can perform Reactome Analysis In a convenient way. The Analysis Type will be chosen depending on your supplied input:

1. If you supply a vector or a single-columned table, "Over-Representation" analysis will be performed.

2. If you supply a multi-column table, with the first column being molecules identifiers and the rest being numeral expression values, "Expression" analysis will be performed.

See the details section for the accepted input types and format.

Usage

rba_reactome_analysis(
  input,
  input_format = NULL,
  projection = TRUE,
  interactors = FALSE,
  species = NULL,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = 1,
  include_disease = TRUE,
  min = NULL,
  max = NULL,
  ...
)

Arguments

Details

You can supply your table or vector input in numerous formats:

1. A R object which can be data frame, matrix or a simple vector.

2. A path to a local text file in your device that contains the molecules data. (The file should be formatted correctly, see below.)

3. A URL pointing to a text file on the web that contains the molecules data. (The file should be formatted correctly, see below.

If you supply a text file (as a local file path or URL), it should be in TSV (Tab-Separated Values) format; Column names should start with "#" character. Note that if you are providing the file for "Over-Representation" analysis (i.e. Single columned-data) this header line is optional and will be used as your 'Sample Name', otherwise it is required.
Also, form the "summary" element in the function's output, you can see how Reactome Interpreted your input and subsequently the type of analysis that has been performed.
There is no strict criteria about the type of your molecules Identifiers, Reactome will Map the IDs to it's internal database entities. Nevertheless, You can check if all your identifiers has been found in "identifiersNotFound" element in the function's output.
After Any Analysis, Reactome will associate a token to your analysis. It can be later used to in function that requires the token (e.g to retrieve the analysis results, download pdf).
Note that Reactome will store your token for only 7 days. You can download your full results with rba_reactome_analysis_download, and re-import it anytime to reactome (using rba_reactome_analysis_import) to generate a new token.

Value

List containing the results and information of your analysis. Note that you can use the token returned in the "summary" sub-list of the results (i.e. results$summary$token) to retrieve your results later or in other Reactome analysis functions.

Corresponding API Resources

"POST https://reactome.org/AnalysisService/identifiers/form"
"POST https://reactome.org/AnalysisService/identifiers/url"
"POST https://reactome.org/AnalysisService/identifiers/form/projection"
"POST https://reactome.org/AnalysisService/identifiers/url/projection"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Analysis Service": rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Other "Enrichment/Over-representation": rba_enrichr(), rba_mieaa_enrich(), rba_panther_enrich(), rba_string_enrichment(), rba_string_enrichment_image()

Examples

## Not run: 
rba_reactome_analysis(input = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42"))

## End(Not run)
## Not run: 
rba_reactome_analysis(input = "c:/rbioapi/genes.txt")

## End(Not run)
## Not run: 
rba_reactome_analysis(input = "https://qazwsx.com/genes.txt")

## End(Not run)

Description

Based on the "request" argument, you can download different analysis results data associated with a given token.

Usage

rba_reactome_analysis_download(
  token,
  request,
  save_to = NULL,
  resource = "TOTAL",
  ...
)

Arguments

Details

Token is associated to each Reactome analysis results and kept by Reactome for at least 7 days. You can locate it in rba_reactome_analysis's output, under a sub-list named "summary" (i.e. results$summary$token).
Use rba_reactome_analysis_pdf to save a full report in PDF format.

Value

NULL, a CSV,JSON or Gzipped JSON file will be saved to disk based on your input.

Corresponding API Resources

GET https://reactome.org/AnalysisService/download/{token}/entities/ found/{resource}/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/entities/ notfound/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/pathways/ {resource}/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/result.json"
GET https://reactome.org/AnalysisService/download/{token}/result.json.gz"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis_pdf rba_reactome_analysis

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

## Not run: 
rba_reactome_analysis_download(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    request = "pathways", save_to = "found_ids.csv")

## End(Not run)
## Not run: 
rba_reactome_analysis_download(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    request = "found_ids", save_to = "found_ids.csv")

## End(Not run)

Description

If you have a JSON file of analysis results (only obtained via rba_reactome_analysis_download with the result argument set to "results", or "results_gz"), you can import the results back to Reactome and retrieve a token.
This is useful when you want to use other Reactome services which require a token but you do not have a token or your token has been expired (i.e. more than 7 days passed from your analysis).

Usage

rba_reactome_analysis_import(input, input_format = NULL, ...)

Arguments

Value

A list containing the new token and other information of your imported results.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/import/"
"GET https://reactome.org/AnalysisService/import/form"
"GET https://reactome.org/AnalysisService/import/url"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

## Not run: 
rba_reactome_analysis_import("c:/rbioapi/res.json")

## End(Not run)
## Not run: 
rba_reactome_analysis_import("https://qaz.com/res.json.gz")

## End(Not run)

Description

Use this function to map molecule identifiers of different species to Reactome Identifiers.

Usage

rba_reactome_analysis_mapping(
  input,
  input_format = NULL,
  projection = TRUE,
  interactors = FALSE,
  ...
)

Arguments

Value

List containing your identifiers and the IDS and resources they are mapped to.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/mapping"
"GET https://reactome.org/AnalysisService/mapping/form"
"GET https://reactome.org/AnalysisService/mapping/form/projection"
"GET https://reactome.org/AnalysisService/mapping"
"GET https://reactome.org/AnalysisService/mapping/url"
"GET https://reactome.org/AnalysisService/mapping/url/projection"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

## Not run: 
rba_reactome_analysis_mapping(c("Q8SQ34", "cd40"))

## End(Not run)

Description

Use this function to save a detailed report of your previous analysis (That you have done with rba_reactome_analysis). You need to supply a 'token' associated to your previous analysis.

Usage

rba_reactome_analysis_pdf(
  token,
  species,
  save_to = NULL,
  number = 25,
  resource = "TOTAL",
  diagram_profile = "Modern",
  analysis_profile = "Standard",
  fireworks_profile = "Barium Lithium",
  ...
)

Arguments

Details

Token is associated to each Reactome analysis results and kept by Reactome for at least 7 days. You can locate it in rba_reactome_analysis's output, under a sub-list named "summary" (i.e. results$summary$token).
Note that Reactome will store your token for only 7 days. You can download your full results with rba_reactome_analysis_download, and re-import it anytime to reactome (using rba_reactome_analysis_import) to generate a new token. Use rba_reactome_analysis_download to save your results in other formats.

Value

NULL, a PDF file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/report/{token}/{species}/ {filename}.pdf"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis_download rba_reactome_analysis

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

## Not run: 
rba_reactome_analysis_pdf(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM%3D",
    species = 9606, save_to = "my_analysis.pdf")

## End(Not run)

Description

Use This function to Compare human's manually-curated pathways and computationally inferred pathways (orthologous) in other species.

Usage

rba_reactome_analysis_species(
  species_dbid,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = 1,
  min = NULL,
  max = NULL,
  ...
)

Arguments

Details

Reactome incorporate manually curated human reactions and PANTHER's protein homology data to Computationally infer events in other eukaryotic species.
In version 73 (11 June 2020), using an orthology-based approach, Homo sapiens events was projected to 18,654 orthologous pathways (with 81,835 orthologous proteins) in 15 non-human species. See Reactome Computationally Inferred Events for more information.

Value

List with the results of the comparison.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/species/homoSapiens/{species}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_orthology

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_token()

Examples

rba_reactome_analysis_species(species_dbid = 48892)

Description

Use a token generated After a Reactome analysis (via rba_reactome_analysis) to Retrieve the analysis results. The output format is identical to the returned object of rba_reactome_analysis.

Usage

rba_reactome_analysis_token(
  token,
  species,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = NULL,
  include_disease = TRUE,
  min = NULL,
  max = NULL,
  ...
)

Arguments

Details

After Any Analysis, Reactome will associate a token to your analysis. It can be later used to in function that requires the token (e.g to retrieve the analysis results, download pdf).
Note that Reactome will store your token for only 7 days. You can download your full results with rba_reactome_analysis_download, and re-import it anytime to reactome (using rba_reactome_analysis_import) to generate a new token.

Value

List containing the results and information of your analysis.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/token/{token}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Analysis Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species()

Examples

## Not run: 
rba_reactome_analysis_token(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    species = 9606)

## End(Not run)

Description

This function will retrieve a list of complexes that include your supplied molecule as a component.

Usage

rba_reactome_complex_list(id, resource, ...)

Arguments

Value

Data frame where each row is a complex containing your supplied molecule and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/complexes/{resource}/ {identifier}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Physical Entity Queries": rba_reactome_complex_subunits(), rba_reactome_entity_other_forms(), rba_reactome_participant_of()

Examples

rba_reactome_complex_list(id = "3845", resource = "NCBI Gene")


rba_reactome_complex_list(id = "P00533", resource = "UniProt")

Description

This function will return a list of subunits which are participants of your supplied complex.

Usage

rba_reactome_complex_subunits(complex_id, exclude_structures = FALSE, ...)

Arguments

Details

Subunits will be returned recursively; Which means that if a subunit was itself a complex, subunit of that complex will be also returned in the results.

Value

Data frame which each row is a subunit of your supplied complex and the columns are pertinent information of that subunit.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/complex/{id}/subunits"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Physical Entity Queries": rba_reactome_complex_list(), rba_reactome_entity_other_forms(), rba_reactome_participant_of()

Examples

rba_reactome_complex_subunits(complex_id = "R-HSA-5674003",
    exclude_structures = FALSE)

Description

This function Retrieve a list of all diseases or disease DOIDs annotated in Reactome.

Usage

rba_reactome_diseases(doid = FALSE, ...)

Arguments

Value

Data frame containing all the disease annotation available at Reactome. If doid was set to TRUE, DOID info will be returned instead.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/diseases"
"GET https://reactome.org/ContentService/data/diseases/doid"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

Examples

rba_reactome_diseases()


rba_reactome_diseases(doid = TRUE)

Description

This function retrieve a list containing all other forms of your supplied Physical Entity ID.

Usage

rba_reactome_entity_other_forms(entity_id, ...)

Arguments

Details

According to Reactome API documentation, "These other forms are Physical Entities that share the same Reference Entity identifier, e.g. PTEN H93R R-HSA-2318524 and PTEN C124R R-HSA-2317439 are two forms of PTEN."

Value

Data frame where each row is other forms of your supplied Entity ID and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/entity/{id}/otherForms"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Physical Entity Queries": rba_reactome_complex_list(), rba_reactome_complex_subunits(), rba_reactome_participant_of()

Examples

rba_reactome_entity_other_forms("R-HSA-199420")

Description

Along with Reactome's events hierarchy, This function will retrieve all the events beginning from your supplied event up to the "Top level Pathway". see "Details section" for more information.

Usage

rba_reactome_event_ancestors(event_id, ...)

Arguments

Details

By Reactome's definition, Events are the building blocks of biological processes and could be of two main classes: "Pathway" or "Reaction-like events". The events are organized in a hierarchical structure; and each event could be child or parent to another event; The hierarchy will always begin with a "Top level pathway" event. Also note that a given event could be part of more that one hierarchies.

Value

List which every element is a Data frame listing your supplied event along with it's ancestor events. Because any given event can be part of more than one pathway hierarchy, the list may contain multiple data frames.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/event/{id}/ancestors"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Queries Related to Events": rba_reactome_event_hierarchy()

Examples

rba_reactome_event_ancestors("R-HSA-5673001")

Description

This function will retrieve the full Events hierarchy of your supplied species. Directly under each species, each child element is a "top Level Pathway". You can traverse the events tree down by following the "children" element.

Usage

rba_reactome_event_hierarchy(species, ...)

Arguments

Details

By Reactome's definition, Events are the building blocks of biological processes and could be of two main classes: "Pathway" or "Reaction-like events". The events are organized in a hierarchical structure; and each event could be child or parent to another event; The hierarchy will always begin with a "Top level pathway" event. Also note that a given event could be part of more that one hierarchies.

Value

List which is a representation of the species's events hierarchy described in the "Details section".

Corresponding API Resources

"GET https://reactome.org/ContentService/data/eventsHierarchy/{species}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Queries Related to Events": rba_reactome_event_ancestors()

Examples

## Not run: 
#very large response!
rba_reactome_event_hierarchy("Homo sapiens")

## End(Not run)
## Not run: 
#very large response!
rba_reactome_event_hierarchy(9606)

## End(Not run)

Description

This function could be called in two scenarios:

1. With create_document = FALSE: To retrieve an image of that event's Diagram.

2. With create_document = TRUE: To retrieve a PDF document with the event's diagram image and additional information.

see "Details section" for more information

Usage

rba_reactome_exporter_diagram(
  event_id,
  save_to = NULL,
  create_document = FALSE,
  resource = "TOTAL",
  diagram_profile = "Modern",
  analysis_profile = "Standard",
  token = NULL,
  exp_column = NULL,
  document_level = 1,
  output_format = "png",
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ehld = FALSE,
  ...
)

Arguments

Details

If the function is called with create_document = FALSE:
The result will be an image with the format supplied in "output_format" argument. If the supplied event ID refers to a pathway, the image's content will be the that pathways diagram. If the supplied event ID refers to a sub-pathway or reaction event, the parent pathway's diagram will be exported, with that reaction or sub-pathway's events highlighted.
Note that to export an image of reaction-like event separately, you should use rba_reactome_exporter_reaction.
If the function is called with create_document = TRUE:
A PDF document will contain an image of the event's diagram and the following information of that events: Summation, Literature references, Edit history type, location, compartments and diseases. note that if you call the function with "document level = 1", information of your supplied event's children will also be included.

Value

NULL, Based to the inputs, an image or PDF file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/diagram/{identifier} .{ext}"
"GET https://reactome.org/ContentService/exporter/document/event/ {identifier}.pdf"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_exporter_reaction rba_reactome_analysis

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_event(), rba_reactome_exporter_overview(), rba_reactome_exporter_reaction()

Examples

## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
  create_document = FALSE)

## End(Not run)
## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
    create_document = FALSE)

## End(Not run)
## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
    create_document = TRUE)

## End(Not run)
## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
    output_format = "svg",
    save_to = "reactome_event_diagram.svg")

## End(Not run)

Description

This function will export a supplied Reactome Event (Pathway or Reaction) to a SBGN (Systems Biology Graphical Notation) or SBML (Systems Biology Markup Language)

Usage

rba_reactome_exporter_event(event_id, output_format, save_to = NULL, ...)

Arguments

Value

NULL, According to the inputs, a SBGN or SBML file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/event/ {identifier}.sbgn"
"GET https://reactome.org/ContentService/exporter/event/ {identifier}.sbml"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_overview(), rba_reactome_exporter_reaction()

Examples

## Not run: 
rba_reactome_exporter_event(event_id = "R-HSA-177929",
    output_format = "sbgn",
    save_to = "R-HSA-177929.sbgn")

## End(Not run)
## Not run: 
rba_reactome_exporter_event(event_id = "R-HSA-177929",
    output_format = "sbgn")

## End(Not run)

Description

This function will Save a Pathway Overview of the supplied specie as an image file.

Usage

rba_reactome_exporter_overview(
  species,
  output_format = "png",
  save_to = NULL,
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  diagram_profile = "Copper",
  token = NULL,
  resource = "TOTAL",
  exp_column = NULL,
  coverage = FALSE,
  ...
)

Arguments

Value

NULL, Based to the inputs, an image file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/fireworks/{species}.{ext}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_event(), rba_reactome_exporter_reaction()

Examples

## Not run: 
rba_reactome_exporter_overview(species = 9606,
    output_format = "svg",
    save_to = "human_pathways.svg")

## End(Not run)
## Not run: 
rba_reactome_exporter_overview(species = 9606,
    token = 123456789)

## End(Not run)

Description

This function will Save a Reactome event of class "ReactionLikeEvent" as an image file.

Usage

rba_reactome_exporter_reaction(
  event_id,
  save_to = NULL,
  output_format = "png",
  resource = "TOTAL",
  diagram_profile = "Modern",
  analysis_profile = "Standard",
  token = NULL,
  exp_column = NULL,
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ...
)

Arguments

Details

Note that this function will save Reaction-like event separately and out of it's parent pathway context. To overlay a Reaction on it's parent pathway, use rba_reactome_exporter_diagram.

Value

NULL, Based to the inputs, an image file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/reaction/ {identifier}.{ext}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_exporter_diagram rba_reactome_analysis

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_event(), rba_reactome_exporter_overview()

Examples

## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
    create_document = FALSE)

## End(Not run)
## Not run: 
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
     output_format = "svg",
     save_to = "reactome_reacion_image.svg")

## End(Not run)

Description

You can call this function in two scenarios: 1- To retrieve information of all available PSICQUIC resources, call the function without providing any argument; i.e rba_reactome_interactors_psicquic(). 2-To retrieve a list of interactors of specific protein(s), fill out the function's arguments.

Usage

rba_reactome_interactors_psicquic(
  proteins = NULL,
  resource = NULL,
  details = TRUE,
  ...
)

Arguments

Value

Depending your input, a list containing the detailed or summary of PSICQUIC interactions or a data frame of all registered PSICQUIC resources.

Corresponding API Resources

"POST https://reactome.org/ContentService/interactors/psicquic/molecules/ {resource}/details"
"POST https://reactome.org/ContentService/interactors/psicquic/molecules/ {resource}/summary"
"GET https://reactome.org/ContentService/interactors/psicquic/resources"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Molecule Interactors": rba_reactome_interactors_static()

Examples

rba_reactome_interactors_psicquic()


rba_reactome_interactors_psicquic(proteins = c("TP53", "MYC"),
    resource = "BioGrid",
    details = FALSE)


rba_reactome_interactors_psicquic(proteins = c("TP53", "MYC"),
    resource = "BioGrid",
    details = TRUE)

Description

Reactome maintain a locally host a version of IntAct(Static) interactions database. Using this function, you can retrieve IntAct information of a protein(s) in two scenarios:

1. If endpoint = "details" or "summary": Retrieve a detailed/summary information of your supplied protein accession(s) from IntAct database.

2. If endpoint = "pathway", Retrieve a list of Reactome pathways which include your supplied protein accession. Pathways with the class "TopLevelPathway" will be excluded.

Usage

rba_reactome_interactors_static(
  proteins,
  endpoint = "details",
  only_diagrammed = FALSE,
  species = NULL,
  ...
)

Arguments

Value

List which it's content varies based on the supplied "endpoint" argument.

Corresponding API Resources

"POST https://reactome.org/ContentService/interactors/static/ molecules/details"
"POST https://reactome.org/ContentService/interactors/static/ molecules/summary"
"GET https://reactome.org/ContentService/interactors/static/ molecules/pathways"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Molecule Interactors": rba_reactome_interactors_psicquic()

Examples

rba_reactome_interactors_static(proteins = "Q9BXM7-1",
    endpoint = "pathways", species = "Homo sapiens")


rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "details")


rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "summary")

Description

By providing an external identifier from a given resource, you can retrieve a list of pathways/reactions that include your supplied ID.

Usage

rba_reactome_mapping(id, resource, map_to, species = "Homo sapiens", ...)

Arguments

Value

Data frame where each row is a pathway/reaction and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/pathways"
"GET https://reactome.org/ContentService/data/mapping/{resource}/ {identifier}/reactions"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

Examples

rba_reactome_mapping(id = "PTEN", resource =  "UniProt",
    map_to = "reactions", species = 9606)

Description

Reactome incorporate manually curated human reactions and PANTHER's protein homology data to Computationally infer events in other eukaryotic species.

Usage

rba_reactome_orthology(event_ids, species_dbid, ...)

Arguments

Details

In version 73 (11 June 2020), using an orthology-based approach, Homo sapiens events was projected to 18,654 orthologous pathways (with 81,835 orthologous proteins) in 15 non-human species.
See Reactome Computationally Inferred Events for more information.

Value

List containing found Orthologous event(s) in your supplied species and their pertinent information.

Corresponding API Resources

"POST https://reactome.org/ContentService/data/orthologies/ids/ species/{speciesId}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis_species

Examples

rba_reactome_orthology(event_ids = c("R-HSA-6799198", " R-HSA-72764"),
    species_dbid = 49633)

Description

This function will retrieve a list of complexes and sets that Your supplied entity ID participates in (e.g. as a complex component, reaction output).

Usage

rba_reactome_participant_of(entity_id, ...)

Arguments

Value

List of Reactome database Entities which Your supplied ID is a participant in them.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/entity/{id}/componentOf"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_participants

Other "Reactome Content Service - Physical Entity Queries": rba_reactome_complex_list(), rba_reactome_complex_subunits(), rba_reactome_entity_other_forms()

Examples

rba_reactome_participant_of(entity_id = "R-HSA-199420")

Description

Participating molecules in a Reactome comprises set of 'Physical Entity' and 'Reference Entities' class objects. Use this function to retrieve all, only 'Physical Entity' or only 'Reference Entities' participants of given event.

Usage

rba_reactome_participants(
  event_id,
  only_physical_entities = FALSE,
  only_reference_entities = FALSE,
  ...
)

Arguments

Details

A 'Physical Entity' Instance could include an individual molecule, a multi-molecular complex or a set of molecule forming a group based on some characteristics. a single molecule can have different 'Physical Entity' instances based on it's associated attributes. For example, IgK Ig kappa chain, has two 'Physical Entity' instances; one, with ID "R-HSA-197041" refers to the secreted antibody protein to the extra-cellular region; And the second one is with ID "R-HSA-2038819" and refers to the plasma-membrane-integrated form of the antibody protein.
To make it possible to link multiple 'Physical Entity' instances of a molecule, Reactome uses a data class named "'Reference Entities'" which correspond to the invariant attribute of a molecule. for example, both of the above-mentioned 'Physical Entities' see a 'Reference Entities' named "UniProt:P01834 IGKC.
See Reactome Data Model for more information about the data model and Physical Entities.

Value

List with the participant of your supplied Event ID. A Data frame if only physical or 'Reference Entities' was requested.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/participants/{id}"
"GET https://reactome.org/ContentService/data/participants/{id}/ participatingPhysicalEntities"
"GET https://reactome.org/ContentService/data/participants/{id}/ referenceEntities"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_participant_of

Examples

rba_reactome_participants("R-HSA-5682012")


rba_reactome_participants("R-HSA-5682012", only_physical_entities = TRUE)


rba_reactome_participants("R-HSA-5682012", only_reference_entities = TRUE)

Description

A Reactome Event could be comprised of other events (meaning, a pathway that include other pathways itself). Use this function to recursively return all the events which reside downstream of your supplied event ID (or an attribute of that events).

Usage

rba_reactome_pathways_events(event_id, attribute_name = NULL, ...)

Arguments

Details

By Reactome's definition, Events are the building blocks of biological processes and could be of two main classes: "Pathway" or "Reaction-like events". The events are organized in a hierarchical structure; and each event could be child or parent to another event; The hierarchy will always begin with a "Top level pathway" event. Also note that a given event could be part of more that one hierarchies.

Value

Data frame where each row is a contained event and columns are event's attributes. If an "attribute_name" argument was supplied, a character vector will be returned.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathway/{id}/ containedEvents"
"GET https://reactome.org/ContentService/data/pathway/{id}/ containedEvents/{attributeName}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Pathway Related Queries": rba_reactome_pathways_low(), rba_reactome_pathways_top()

Examples

rba_reactome_pathways_events(event_id = "R-HSA-5673001")


rba_reactome_pathways_events(event_id = "R-HSA-5673001",
    attribute_name = "displayName")

Description

Use this function to search the event hierarchy and retrieve a list of all lower level pathways (non TopLevelPathway class) that contain a given 'Physical Entity' or Event. See "Arguments section" on how to modify your search.

Usage

rba_reactome_pathways_low(
  entity_id,
  with_diagram = FALSE,
  all_forms = FALSE,
  species = NULL,
  ...
)

Arguments

Value

Data frame where each row is a pathway that contains your supplied entity and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathways/low/entity/{id}"
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/{id}"
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/{id}/allForms"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Pathway Related Queries": rba_reactome_pathways_events(), rba_reactome_pathways_top()

Examples

rba_reactome_pathways_low(entity_id = "R-HSA-199420")


rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE)


rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE,
    all_forms = TRUE)

Description

This function will Return a list of all pathways with the class "TopLevelPathway" which are annotated in your supplied species.

Usage

rba_reactome_pathways_top(species, ...)

Arguments

Details

Reactome's Events hierarchy for any specie will begin with pathways with class "TopLevelPathway" (e.g. "Immune System", "Metabolism of proteins"). further down in the event's hierarchy tree, each TopLevelPathway has has other events itself (e.g. "Adaptive immune system", "Innate immune system"). Based on the chosen pathway, the hierarchy tree would typically goes further down.

Value

Data frame where each row is a Top Level Pathway and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathways/top/{species}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Pathway Related Queries": rba_reactome_pathways_events(), rba_reactome_pathways_low()

Examples

rba_reactome_pathways_top(species = 9606)


rba_reactome_pathways_top(species = "Saccharomyces cerevisiae")

Description

A person by his identifiers

Usage

rba_reactome_people_id(
  person_id,
  authored_pathways = FALSE,
  publications = FALSE,
  attribute_name = NULL,
  ...
)

Arguments

Value

List containing the requested informations of your supplied person.

Corresponding API Resources

"GET https://reactome.org/ContentService"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Person Queries": rba_reactome_people_name()

Examples

rba_reactome_people_id("391309")


rba_reactome_people_id(person_id = "391309", authored_pathways = TRUE)

Description

Using this function you can query people by partially matching or exact name and retrieve a list of matching people in Reactome.

Usage

rba_reactome_people_name(person_name, exact_match = FALSE, ...)

Arguments

Value

List where each element is a search hit contains the person's information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/people/name/{name}"
"GET https://reactome.org/ContentService/data/people/name/{name}/exact"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

Other "Reactome Content Service - Person Queries": rba_reactome_people_id()

Examples

rba_reactome_people_name("Jupe")


rba_reactome_people_name("Steve Jupe", exact_match = TRUE)

Description

Using this Comprehensive function, You can Retrieve any object from Reactome knowledge-base

Usage

rba_reactome_query(
  ids,
  enhanced = FALSE,
  map = FALSE,
  attribute_name = NULL,
  ...
)

Arguments

Value

List containing your query outputs.

Corresponding API Resources

"POST https://reactome.org/ContentService/data/query/ids"
"POST https://reactome.org/ContentService/data/query/ids/map"
"GET https://reactome.org/ContentService/data/query/{id}"
"GET https://reactome.org/ContentService/data/query/enhanced/{id}"
"GET https://reactome.org/ContentService/data/query/{id}/{attributeName}"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

Examples

rba_reactome_query(ids = c("8953958", "11982506", "R-ALL-9649879"))


rba_reactome_query(ids = "R-HSA-9656256", enhanced = TRUE)


rba_reactome_query(ids = "8863054", attribute_name = "displayName")

Description

Use this function to retrieve a table of Available species in Reactome.

Usage

rba_reactome_species(only_main = FALSE, ...)

Arguments

Value

Data frame where each row is a species and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/species/all"
"GET https://reactome.org/ContentService/data/species/main"

References

• Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

• Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

• Reactome Content Services API Documentation

• Citations note on Reactome website

Examples

rba_reactome_species()


rba_reactome_species(only_main = TRUE)