mabsGO: MeanAbs Enrichment Analysis for GO

View source: R/mabsAnalyser.R

mabsGOR Documentation

MeanAbs Enrichment Analysis for GO

Description

MeanAbs enrichment analysis with GO terms.

Usage

mabsGO(
  geneList,
  ont = "BP",
  OrgDb,
  keyType = "SYMBOL",
  nPerm = 1000,
  minGSSize = 5,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH"
)

Arguments

geneList

named numeric vector with gene SYMBOLs in the name slot decreasingly ranked by scores in the data slot.

ont

one of "BP", "MF", "CC" or "ALL"

OrgDb

OrgDb

keyType

keytype of gene

nPerm

permutation numbers

minGSSize

integer, minimum size of each gene set in annotation system

maxGSSize

integer, maximum size of each gene set in annotation system

pvalueCutoff

pvalue cutoff

pAdjustMethod

pvalue adjustment method

Value

feaResult object

Author(s)

Yuzhu Duan

Examples

data(targetList)
#mg <- mabsGO(geneList=targetList, ont="MF", OrgDb="org.Hs.eg.db",
#             pvalueCutoff=1)
#head(mg)

yduan004/signatureSearch documentation built on Feb. 19, 2024, 9:30 a.m.