GSEA: GSEA

In GuangchuangYu/clusterProfiler: A universal enrichment tool for interpreting omics data

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",
  gson = NULL,
  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	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
gson	a GSON object, if not NULL, use it as annotation data.
TERM2GENE	user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene. Only used when gson is NULL.
TERM2NAME	user input of TERM TO NAME mapping, a data.frame of 2 column with term and name. Only used when gson is NULL.
verbose	logical
seed	logical
by	one of 'fgsea' or 'DOSE'
...	other parameter

Value

gseaResult object

Author(s)

Guangchuang Yu https://yulab-smu.top

GuangchuangYu/clusterProfiler documentation built on Nov. 30, 2024, 3:25 a.m.