Description Usage Arguments Value Author(s)
Gene Set Enrichment Analysis of Reactome Pathway
1 2 3 | gsePathway(geneList, organism = "human", exponent = 1, nPerm = 1000,
minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05,
pAdjustMethod = "BH", verbose = TRUE, seed = FALSE, by = "fgsea")
|
geneList |
order ranked geneList |
organism |
organism |
exponent |
weight of each step |
nPerm |
permutation numbers |
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 |
seed |
logical |
by |
one of 'fgsea' or 'DOSE' |
gseaResult object
Yu Guangchuang
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