gsePathway: gsePathway

In GuangchuangYu/ReactomePA: Reactome Pathway Analysis

gsePathway

Description

Gene Set Enrichment Analysis of Reactome Pathway

Usage

gsePathway(
  geneList,
  organism = "human",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

geneList	order ranked geneList
organism	organism
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of each geneSet for analyzing
eps	This parameter sets the boundary for calculating the p value.
pvalueCutoff	pvalue Cutoff
pAdjustMethod	pvalue adjustment method
verbose	print message or not
seed	logical
by	one of 'fgsea' or 'DOSE'
...	other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

GuangchuangYu/ReactomePA documentation built on Oct. 31, 2024, 9:26 a.m.