This function which will retrieve the enrichment results of your supplied gene-list id against one or multiple Enrichr libraries.

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

Arguments

user_list_id

An ID returned to you after uploading a gene list using rba_enrichr_add_list

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

Note that using rba_enrichr is a more convenient way to automatically perform this and other required function calls to enrich your input gene-set.

Corresponding API Resources

"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

if (FALSE) {
rba_enrichr_enrich(user_list_id = "11111")
}
if (FALSE) {
rba_enrichr_enrich(user_list_id = "11111",
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)
}
if (FALSE) {
rba_enrichr_enrich(user_list_id = "11111",
    gene_set_library = "go",
    regex_library_name = TRUE)
}