I was using Org.hs.eg.db
-type objects to create an annotation map with annotate
package in a following way:
symbol.bimap <- getAnnMap("SYMBOL", "org.hs.eg.db")
. By default, the returned bimap uses ENTREZ ids as keys. I want to use ENSEMBL ids as keys, but apparently getAnnMap
does not allow for that (and I need a bimap object downstream). This link suggested to use EnsDb objects from ensembldb
package, but I cannot somehow get EnsDb object to work with getAnnMap
function. Returned error is:
getAnnMap("SYMBOL", "EnsDb.Hsapiens.v86")
Error in .select(x = x, keys = keys, columns = columns, keytype = keytype, :
Argument keytype is mandatory if keys is a character vector!
Is there any straightforward way to return a bimap between ENSEMBL and SYMBOL keys, or I need to create it via other functions (mapIds or what not)?