rba_enrichr_enrich {rbioapi}R Documentation

Get Enrichr Enrichment Results

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 = FALSE,
  organism = "human",
  background_id = NULL,
  progress_bar = TRUE,
  ...
)

Arguments

user_list_id

An ID returned after uploading a gene list using rba_enrichr_add_list, with the 'speedrichr' set to TRUE or FALSE depending on whether you intend to analyze this gene list with or without a background gene list, respectively.

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: (default = FALSE) if TRUE 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). If 'background_id' is provided, the only available option is "human".

background_id

An ID returned after uploading a background gene list using rba_enrichr_add_background

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

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

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)


[Package rbioapi version 0.8.3 Index]