getting mouse gene ids from makeTxDbFromUCSC()
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warrena • 0
@warrena-16186
Last seen 4.4 years ago

I am trying to get mm10 gene annotations with gene names. I have tried the following:

ncbiRefSeq = makeTxDbFromUCSC(genome="mm10", tablename="ncbiRefSeq")
geneid = makeTxDbFromUCSC(genome="mm10", tablename="geneid")

knownGene = makeTxDbFromUCSC(genome="mm10", tablename="knownGene")

In the first two cases, I get no gene names: Type of Gene ID: no gene ids

In the third case (knownGene), I get Entrez Gene ID numeric identifiers. Is there a way to get the standard gene name identifiers? Assistance/advice would be greatly appreciated.

 

GenomicFeatures makeTxDbFromUCSC • 854 views
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shepherl 3.4k
@lshep
Last seen 3 hours ago
United States

There are some annotation packages you can use like the TxDb.Mmusculus.UCSC.mm10.knownGene or Mus musculus package that already has the TxDb or OrgDb objects created.

Perhaps something like the following is what you are looking for:

library(Mus.musculus)
genes(Mus.musculus, columns = c("ENTREZID","ALIAS", "SYMBOL"))
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