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

Marc Carlson mcarlson at fhcrc.org
Thu Oct 31 22:45:27 CET 2013

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:


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:


I hope this helps,


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
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list