GSEA {clusterProfiler} | R Documentation |
a universal gene set enrichment analysis tools
GSEA(geneList, exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", TERM2GENE, TERM2NAME = NA, verbose = TRUE, seed = FALSE, by = "fgsea")
geneList |
order ranked geneList |
exponent |
weight of each step |
nPerm |
number of permutations |
minGSSize |
minimal size of each geneSet for analyzing |
maxGSSize |
maximal size of genes annotated for testing |
pvalueCutoff |
pvalue cutoff |
pAdjustMethod |
p value adjustment method |
TERM2GENE |
user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene |
TERM2NAME |
user input of TERM TO NAME mapping, a data.frame of 2 column with term and name |
verbose |
logical |
seed |
logical |
by |
one of 'fgsea' or 'DOSE' |
gseaResult object
Guangchuang Yu