rba_enrichr_add_list {rbioapi}R Documentation

Upload Your Gene-List to Enrichr

Description

This function uploads your gene list to Enrichr and retrieves a unique 'user list ID' required for performing enrichment analysis.

Usage

rba_enrichr_add_list(
  gene_list,
  description = NULL,
  organism = "human",
  speedrichr = FALSE,
  ...
)

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.

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).

speedrichr

logical (default = FALSE) Set to TRUE if you will use this gene list with a background list; otherwise, set to FALSE. Only available for human libraries. Refer to the details section for more information.

...

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

Details

Enrichr uses separate APIs for analysis with or without a background gene list. Set 'speedrichr = TRUE' if this gene list will be used with a background gene list; otherwise, set it to FALSE. Gene lists submitted with 'speedrichr = TRUE' can only be analyzed with a background set, and those submitted with 'speedrichr = FALSE' can only be analyzed without one. Currently, background-based enrichment is supported only for human libraries.

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 with the unique IDs for your uploaded gene list. 'userListId' is the ID required for later steps.

Corresponding API Resources

"POST https://maayanlab.cloud/Enrichr/addList"
"POST https://maayanlab.cloud/speedrichr/api/addList"

References

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples


rba_enrichr_add_list(gene_list = c("TP53", "TNF", "EGFR"),
     description = "tumoral genes",
     speedrichr = FALSE)


rba_enrichr_add_list(gene_list = c("RAG1", "RAG2", "DNTT", "LIG4", "ARTEMIS"),
     description = "TCR rearrangment",
     speedrichr = TRUE)



[Package rbioapi version 0.8.2 Index]