I have gone through the vignette and parts of the reference manual but I am still stuck.
I have a vector of gene symbols, call this vector “Vec”. These are all the genes which expression levels I have measured with RNA-Seq. Subsequently, I want to perform gene set enrichment analysis with GO biological processes terms using a custom script on the differentially expressed genes and to do so, I need a comprehensive list of gene sets induced from Vec. (i.e. I need a list all the gene sets that each could form a subset of Vec, with each gene set classified according to GO biological processes terms. )
To do so, I run the following line:
Gs=GeneSetCollection(Vec, idType = SymbolIdentifier('org.Mm.eg.db'), setType=GOCollection(ontology='BP'))
But I got the following error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘GeneSetCollection’ for signature ‘"character", "SymbolIdentifier", "GOCollection"’
‘org.Mm.eg.db’ definitely contains mapping from Symbols to entrez gene and vice versa.
Is my approach even somewhat correct?
Junren Sia, PhD
Institute of Medical Biology