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GSEA

GSEA

Description

a universal gene set enrichment analysis tools

Usage

GSEA(
  geneList,
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  TERM2GENE,
  TERM2NAME = NA,
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

geneList

order ranked geneList
exponent

weight of each step
minGSSize

minimal size of each geneSet for analyzing
maxGSSize

maximal size of genes annotated for testing
eps

This parameter sets the boundary for calculating the p value.
pvalueCutoff

adjusted pvalue cutoff
pAdjustMethod

p value adjustment method
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
verbose

logical
seed

logical
by

one of 'fgsea' or 'DOSE'
...

other parameter

Value

gseaResult object

Author(s)

Guangchuang Yu

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Initial release

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