Question: getting mouse gene ids from makeTxDbFromUCSC()
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gravatar for warrena
8 months ago by
warrena0
warrena0 wrote:

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.

 

ADD COMMENTlink modified 8 months ago by shepherl ♦♦ 1.3k • written 8 months ago by warrena0
Answer: getting mouse gene ids from makeTxDbFromUCSC()
0
gravatar for shepherl
8 months ago by
shepherl ♦♦ 1.3k
United States
shepherl ♦♦ 1.3k wrote:

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"))
ADD COMMENTlink written 8 months ago by shepherl ♦♦ 1.3k
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