Question: How to create bimap with getAnnMap using ENSEMBL ids instead of ENTREZ?
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gravatar for Pawel Szczesny
7 months ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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)?

annotation bioconductor R • 300 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by Pawel Szczesny3.2k
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