gseDO: DO Gene Set Enrichment Analysis

In aiminy/ModifiedDOSE: Disease Ontology Semantic and Enrichment analysis

Description

perform gsea analysis

Usage

gseDO(geneList, exponent = 1, nPerm = 1000, minGSSize = 10,
  maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH",
  verbose = TRUE, seed = FALSE, by = "fgsea")

Arguments

geneList	order ranked geneList
exponent	weight of each step
nPerm	permutation numbers
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of each geneSet for analyzing
pvalueCutoff	pvalue Cutoff
pAdjustMethod	p value adjustment method
verbose	print message or not
seed	logical
by	one of 'fgsea' or 'DOSE'

Value

gseaResult object

Author(s)

Yu Guangchuang

aiminy/ModifiedDOSE documentation built on May 10, 2019, 7:36 a.m.