[BioC] Coverage by base

[Hervé Pagès]

Hi Rohan,

On 11-10-11 11:49 AM, rohan bareja wrote:
> Hi,
> Ya thats correct..I have summed up the
>   reads using viewSums but I want to get the gene information .Hi,
> I found this archive from bioconductor-sig-sequencing mailing list where they have discussed about cov_by_gene<- Views(cov, genes)
> viewSums(cov_by_gene)https://stat.ethz.ch/pipermail/bioc-sig-sequencing/attachments/20110723/b9f2c69c/attachment.pl
> But I am not sure what is the object "genes" that has been used along with the coverage.Thats exactly what I would like to do.

I think 'genes' is a GRanges object object that was obtained with
something like (pseudo-code):

   library(GenomicFeatures)
   txdb <- makeTranscriptDbFromUCSC(...)
   gene_ranges <- range(transcriptsBy(txdb, by="gene"))
   genes <- unlist(gene_ranges)

Before the unlist() it's always good to make sure that
there is exactly one range per gene e.g. with
table(elementLengths(gene_ranges)). If that's the case
then unlisting will preserve the nb of elements.

Cheers,
H.

>
> Thanks,Rohan
> 	[[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


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319