rba_enrichr {rbioapi}R Documentation

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

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

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.

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

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)



[Package rbioapi version 0.8.2 Index]