gseReactome: Modified GSEA with Reactome

View source: R/gseAnalyzer2.R

gseReactomeR Documentation

Modified GSEA with Reactome

Description

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

Usage

gseReactome(
  geneList,
  organism = "human",
  exponent = 1,
  nPerm = 1000,
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  readable = FALSE
)

Arguments

geneList

order ranked geneList

organism

one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".

exponent

integer value used as exponent in GSEA algorithm.

nPerm

integer defining the number of permutation iterations for calculating p-values

minGSSize

minimal size of each geneSet for analyzing

maxGSSize

maximal size of each geneSet for analyzing

pvalueCutoff

pvalue Cutoff

pAdjustMethod

pvalue adjustment method

verbose

print message or not TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

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 Reactome enrichment
data(geneList, package="DOSE")
#geneList[100:length(geneList)]=0
#rc <- gseReactome(geneList=geneList, pvalueCutoff=1)

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