gseReactome {signatureSearch} | R Documentation |
This modified Gene Set Enrichment Analysis (GSEA) of Reactome pathways supports gene test sets with large numbers of zeros.
gseReactome( geneList, organism = "human", exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE, readable = FALSE )
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. |
feaResult object
# Gene Entrez id should be used for Reactome enrichment data(geneList, package="DOSE") #geneList[100:length(geneList)]=0 #rc <- gseReactome(geneList=geneList, pvalueCutoff=1)