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A One-step Wrapper for Gene-list Enrichment Using Enrichr

Source: R/enrichr.R
rba_enrichr.Rd

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

gene_list

A character vector with Entrez gene symbols of test genes.

description

(optional) A description to be associated with your uploaded gene-set to Enrichr servers.

gene_set_library

One of the:

  1. "all" to select all of the available Enrichr gene-set libraries.

  2. A gene-set library name. You can retrieve the available options for a given species using rba_enrichr_libs.

  3. If regex_library_name = TRUE, A partially-matching name a regex pattern that correspond to one or more of Enrichr library names.

regex_library_name

logical: if TRUE (default) the supplied gene_set_library will be considered as a regex pattern. If FALSE, gene_set_library will be considered as an exact match.

organism

(default = "human") Which model organism version of Enrichr to use? Available options are: "human", (H. sapiens & M. musculus), "fly" (D. melanogaster), "yeast" (S. cerevisiae), "worm" (C. elegans) and "fish" (D. rerio).

background_genes

A character vector of Entrez gene symbols of the background genes.

progress_bar

logical: (default = TRUE) if multiple Enrichr libraries are selected, should a progress bar be displayed?

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

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

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

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

if (FALSE) { # \dontrun{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"))
} # }
# \donttest{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)
# }
# \donttest{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "go",
    regex_library_name = TRUE)
# }