gseGO2: Modified GSEA with GO Terms

View source: R/gseAnalyzer2.R

gseGO2R Documentation

Modified GSEA with GO Terms

Description

This modified Gene Set Enrichment Analysis (GSEA) of GO terms supports gene test sets with large numbers of zeros.

Usage

gseGO2(
  geneList,
  ont = "BP",
  OrgDb,
  keyType = "SYMBOL",
  exponent = 1,
  nproc = 1,
  nPerm = 1000,
  minGSSize = 2,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE
)

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, e.g., "org.Hs.eg.db".

keyType

keytype of gene

exponent

weight of each step

nproc

if not equal to zero, sets BPPARAM to use nproc workers (default = 1)

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

verbose

print message or not

Value

feaResult object

Examples

data(targetList)
# gsego <- gseGO2(geneList=targetList, ont="MF", OrgDb="org.Hs.eg.db",
#                 pvalueCutoff=1)
# head(gsego)

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