enrichMeSH {meshes} | R Documentation |
MeSH term enrichment analysis
enrichMeSH(gene, MeSHDb, database = "gendoo", category = "C", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500)
gene |
a vector of entrez gene id |
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" |
pvalueCutoff |
Cutoff value of pvalue. |
pAdjustMethod |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe |
background genes |
qvalueCutoff |
qvalue cutoff |
minGSSize |
minimal size of genes annotated by Ontology term for testing. |
maxGSSize |
maximal size of genes annotated for testing |
An enrichResult
instance.
Guangchuang Yu
class?enrichResult
## Not run: data(geneList, package="DOSE") de <- names(geneList)[1:100] x <- enrichMeSH(de, MeSHDb = "MeSH.Hsa.eg.db", database='gendoo', category = 'C') ## End(Not run)