YuLab-SMU/meshes

background gene set for enrichMesh isn't working

ymkng opened this issue · 2 comments

ymkng commented

I was wondering what "universe" for enrichMesh function accepts as an input as it isn't specified in the documentation found on bioconductor.

library(meshes)
x <- enrichMeSH(my.geneID3[,3], MeSHDb = "MeSH.Hsa.eg.db", database='gene2pubmed', category = 'C',universe = univ.geneID3[,2])

here, univ.geneID3[,2] is a list of entrez gene ids but I get the error

Error in validObject(.Object) :
invalid class "enrichResult" object: invalid object for slot "universe" in class "enrichResult": got class "integer", should be or extend class "character"

thanks so much!

michelle

GuangchuangYu commented

got class "integer", should be or extend class "character"

as.character(univ.geneID3[,2])

will solve this issue. Gene ID should be in character.

ymkng commented