gseGO2: Modified GSEA with GO Terms

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

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)

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