gseKEGG2: Modified GSEA with KEGG

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

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)

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