mabsReactome {signatureSearch} | R Documentation |
MeanAbs enrichment analysis with Reactome pathways.
mabsReactome( geneList, organism = "human", nPerm = 1000, minGSSize = 5, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", readable = FALSE )
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. |
feaResult
object
# Gene Entrez id should be used for Reactome enrichment data(geneList, package="DOSE") #geneList[100:length(geneList)]=0 #rc <- mabsReactome(geneList=geneList, pvalueCutoff = 1)