gseDO: DO Gene Set Enrichment Analysis

In GuangchuangYu/DOSE: Disease Ontology Semantic and Enrichment analysis

DO Gene Set Enrichment Analysis

Description

perform gsea analysis

Usage

gseDO(
  geneList,
  ont = "HDO",
  organism = "hsa",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

Arguments

geneList	order ranked geneList
ont	one of "HDO", "HPO" or "MPO"
organism	one of "hsa" and "mmu"
exponent	weight of each step
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'
...	other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

GuangchuangYu/DOSE documentation built on Oct. 31, 2024, 9:15 a.m.