gseMeSH {meshes} | R Documentation |
Gene Set Enrichment Analysis of MeSH
gseMeSH( geneList, MeSHDb, database = "gendoo", category = "C", exponent = 1, minGSSize = 10, maxGSSize = 500, eps = 1e-10, pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE, seed = FALSE, by = "fgsea", ... )
geneList |
order ranked geneList |
MeSHDb |
MeSHDb |
database |
one of 'gendoo', 'gene2pubmed' or 'RBBH' |
category |
one of "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L","M", "N", "V", "Z" |
exponent |
weight of each step |
minGSSize |
minimal size of each geneSet for analyzing |
maxGSSize |
maximal size of genes annotated for testing |
eps |
This parameter sets the boundary for calculating the p value. |
pvalueCutoff |
pvalue Cutoff |
pAdjustMethod |
pvalue adjustment method |
verbose |
print message or not |
seed |
logical |
by |
one of 'fgsea' or 'DOSE' |
... |
other parameter |
gseaResult object
Yu Guangchuang
## Not run: data(geneList, package="DOSE") y <- gseMeSH(geneList, MeSHDb = "MeSH.Hsa.eg.db", database = 'gene2pubmed', category = "G") ## End(Not run)