gseKEGG {clusterProfiler} | R Documentation |
Gene Set Enrichment Analysis of KEGG
gseKEGG(geneList, organism = "hsa", keyType = "kegg", exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE, use_internal_data = FALSE, seed = FALSE, by = "fgsea")
geneList |
order ranked geneList |
organism |
supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType |
one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
exponent |
weight of each step |
nPerm |
permutation numbers |
minGSSize |
minimal size of each geneSet for analyzing |
maxGSSize |
maximal size of genes annotated for testing |
pvalueCutoff |
pvalue Cutoff |
pAdjustMethod |
pvalue adjustment method |
verbose |
print message or not |
use_internal_data |
logical, use KEGG.db or latest online KEGG data |
seed |
logical |
by |
one of 'fgsea' or 'DOSE' |
gseaResult object
Yu Guangchuang