gseKEGG2: Modified GSEA with KEGG

View source: R/gseAnalyzer2.R

gseKEGG2R Documentation

Modified GSEA with KEGG

Description

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

Usage

gseKEGG2(
  geneList,
  organism = "hsa",
  keyType = "kegg",
  exponent = 1,
  nproc = 1,
  nPerm = 1000,
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  readable = FALSE
)

Arguments

geneList

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

organism

supported organism listed in URL: http://www.genome.jp/kegg/catalog/org_list.html

keyType

one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'

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

readable

TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

Value

feaResult object

Examples

# Gene Entrez id should be used for KEGG enrichment
data(geneList, package="DOSE")
#geneList[100:length(geneList)]=0
#gsekk <- gseKEGG2(geneList=geneList, pvalueCutoff = 1)
#head(gsekk)

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