This function is an easy-to-use wrapper for the multiple function calls necessary to enrich a given gene-list using Enrichr. see details section for more information.

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

Arguments

gene_list

A vector with Entrez gene symbols.

description

(optional) A name or 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 existed in the results retrieved via 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 regarded as a regex or partially matching name. if FALSE, gene_set_library will be considered 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).

progress_bar

logical: In case of selecting multiple Enrichr libraries, 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 neccessary) Call rba_enrichr_libs to obtain a list of available libraries in Enrichr.

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

  3. Call rba_enrichr_enrich to enrich the gene-list against one or multiple Enrichr libraries

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/datasetStatistics"
"POST https://maayanlab.cloud/Enrichr/addList"
"GET https://maayanlab.cloud/Enrichr/enrich"

References

  • Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;128(14).

  • Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377.

  • Enrichr API Documentation

See also

Examples

# \donttest{
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)
# }