[BioC] extracting SNPs in a given region

[Vincent Carey]

keep the replies on the list.  read the posting guide.  what aspect of

> biocLite("SNPlocs.Hsapiens.dbSNP.20071016")
Running biocinstall version 2.3.13 with R version 2.8.0
Your version of R requires version 2.3 of Bioconductor.
trying URL 'http://bioconductor.org/packages/2.3/data/annotation/bin/macosx/universal/contrib/2.8/SNPlocs.Hsapiens.dbSNP.20071016_0.99.1.tgz'
Content type 'application/x-gzip' length 62173196 bytes (59.3 Mb)
opened URL

isn't working for you?   please supply sessionInfo() result.


On Fri, Jun 5, 2009 at 6:31 PM, Kay Jaja<kjaja27 at yahoo.com> wrote:
> Hi,
>
> Thanks for the info but I tried to download the package and it says that it
> is not available, am I missing somthing?
>
> thanks for your help
>
> ________________________________
> From: Vincent Carey <stvjc at channing.harvard.edu>
> To: Kay Jaja <kjaja27 at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Thursday, June 4, 2009 6:41:57 PM
> Subject: Re: [BioC] extracting SNPs in a given region
>
> there are various approaches.  the most immediately relevant packages are
> the
> SNPlocs.* packages from the annotation/metadata package set.
>
> if you do library(SNPlocs.Hsapiens.dbSNP.20071016) [a more recent
> image is available with a different name, last component beginning 2008],
> you can then do
>
>> c1 = getSNPlocs("chr1")
>> c1[1:10,]
>    RefSNP_id alleles_as_ambig    loc
> 1    4109793                K 115261
> 2    3926102                M 118514
> 3    3926103                Y 118548
> 4    3926104                K 118592
> 5    3926105                Y 118661
> 6    4081096                Y 161648
> 7   28855133                S 221411
> 8   28828438                K 221413
> 9    9730150                R 222312
> 10   3936964                Y 541148
>
> some programming can be used to get indices of SNP for which
> loc lies in your regions
>
> On Thu, Jun 4, 2009 at 6:13 PM, Kay Jaja <kjaja27 at yahoo.com> wrote:
>>
>> Hi All,
>>
>> I have a list of regions on the genome and I am looking  to find the list
>> of SNPs in each region. Is there an R package that can help me to do that.
>>
>> Thanks for the Help
>>
>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> --
> Vincent Carey, PhD
> Biostatistics, Channing Lab
> 617 525 2265
>
>



-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265