On Jan 1, 2012 3:02 AM, <bioconductor-request@r-project.org> wrote:
>
> Send Bioconductor mailing list submissions to
>        bioconductor@r-project.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        https://stat.ethz.ch/mailman/listinfo/bioconductor
> or, via email, send a message with subject or body 'help' to
>        bioconductor-request@r-project.org
>
> You can reach the person managing the list at
>        bioconductor-owner@r-project.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioconductor digest..."
>
>
> Today's Topics:
>
>   1. mapping snp array probe to a gene, biomaRt or others?
>      (Xiaokuan Wei)

I usually pull gene boundaries from a biomaRt and put them in a RangedData
object (from the IRanges package). If your snps are similarly organized,
then the findOverlaps function will get you a reasonable answer. The
genoset package has a better way to summarize copy number by gene, given a
RangedData of gene boundaries. Please check out the end of the genoset
vignette.

Regards, Pete Haverty

>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 31 Dec 2011 15:19:06 -0800
> From: Xiaokuan Wei <weixiaokuan@yahoo.com>
> To: bioconductor <bioconductor@stat.math.ethz.ch>
> Subject: [BioC] mapping snp array probe to a gene, biomaRt or others?
> Message-ID:
>        <1325373546.55508.YahooMailNeo@web114208.mail.gq1.yahoo.com>
> Content-Type: text/plain
>
> Dear List:
>
> Happy New Year!
>
> I have a question regarding mapping the gene to a copy number variations.
>
> I have affy 250 nsp mapping arrays results. Now I try to map the result
for each probe to a gene.
> then, I can perform correlation analysis between the copy number
variation and gene expression level for candidate genes.
>
> I think I have an idea to map expression levels to each gene; but I don't
know how to map copy number variation values to each gene.
> Should I just parse the annotation file of
"Mapping250K_Nsp.na32.annot.csv" to match each probe to a gene symbol? or
there are some other ways.
> Which tools would you recommend?
>
> Any suggestion will be appreciated. Thank you.
>
> -Xiaokuan
>        [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> End of Bioconductor Digest, Vol 107, Issue 1
> ********************************************

	[[alternative HTML version deleted]]

