mabsGO: MeanAbs Enrichment Analysis for GO

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.