[BioC] How to get length information for mm10 genome and geneID gene Symbol?

[Marc Carlson]

Hi Thanh,

I don't speak for GOSeq specifically.  But just very generally if you 
just want to know the length information for the mm10 genome you could 
download a transcriptome package and look at the seq lengths for it.  
Like this:

library("Mus.musculus")
seqlengths(Mus.musculus)

And to get lookup the geneID from the gene symbol you could do it like this

symbols <- c('Cryba1','Cryba4','Cryga','Crygb','Crygc','Crygd')
select(Mus.musculus, keys=symbols, columns='ENTREZID',keytype='ALIAS')
## OR if you feel more confident that these are official gene symbols 
then do it like this:
select(Mus.musculus, keys=symbols, columns='ENTREZID',keytype='SYMBOL')

If you then want gene lengths you can get that too using genes() like this:

genes(TxDb.Mmusculus.UCSC.mm10.knownGene)


I hope this helps,


  Marc



On 10/24/2013 10:35 AM, Thanh Hoang wrote:
> Hi,
> I have a  problem when working with GOSeq. There is support for mm10 genome but not Gene ID geneSymbol
> I am trying to get length information by following the Goseq manual but I still dont understand. So, could you please show me a little details how to get the length information for mm10 genome and geneID geneSymbol ?
>
>> genes = as.integer(all.genes %in% F.genes)
>> names(genes) = all.genes
>> head(genes)
> Cryba1 Cryba4 Cryga Crygb Crygc Crygd
> 1 1 1 1 1 1
>> pwf=nullp(genes,"mm10", "geneSymbol")
> Can't find mm10/geneSymbol length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes.
> Error in value[[3L]](cond) :
> Length information for genome mm10 and gene ID geneSymbol is not available. You will have to specify bias.data manually.
> Thank you so much for your help
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>
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