mabsReactome: MeanAbs Enrichment Analysis for Reactome

View source: R/mabsAnalyser.R

mabsReactomeR Documentation

MeanAbs Enrichment Analysis for Reactome

Description

MeanAbs enrichment analysis with Reactome pathways.

Usage

mabsReactome(
  geneList,
  organism = "human",
  nPerm = 1000,
  minGSSize = 5,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  readable = FALSE
)

Arguments

geneList

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

organism

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

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

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 <- mabsReactome(geneList=geneList, pvalueCutoff = 1)

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