run_gsea {GenomicSuperSignature}R Documentation

GSEA on pre-ordered gene lists

Description

This function is a wrapper of GSEA function, making it applicable to a list of gene lists. Set seed for reproducible result.

Usage

run_gsea(
  geneList,
  TERM2GENE,
  TERM2NAME,
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  verbose = FALSE,
  ...
)

Arguments

geneList

A list of genes ordered by rank

TERM2GENE

User input annotation of TERM TO GENE mapping, a data frame of 2 column with term and gene

TERM2NAME

User input of TERM TO NAME mapping, a data.frame of 2 column with term and name. Optional.

minGSSize

A mininum size of gene set to be analyzed

maxGSSize

A maximum size of gene set to be analyzed

pvalueCutoff

p-value cutoff

verbose

Logical. Default is FALSE

...

Any additional argument inherited from GSEA.

Value

A list of gseaResult objects. If there is no enrichment result, NA will be returned.


[Package GenomicSuperSignature version 1.2.1 Index]