[BioC] Strange output in GenABEL convert.snp.ped()

[Paul Geeleher]

Whoops, apologies, I was sure it was a bioconductor package! I'll
follow your advice indeed.

Paul

On Wed, Feb 10, 2010 at 2:10 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 02/10/2010 05:36 AM, Paul Geeleher wrote:
>> Hi,
>>
>> I'm loading HapMap III data from here:
>> ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/
>
> Hi Paul -- Others might offer more helpful advice, but since GenABEL is
> not a Bioconductor package; have you tried contacting the maintainer?
>
>  packageDescription("genABEL")
>
> Martin
>
>>
>> Basically my code is as follows:
>>
>> setwd('/where/ped/and/map/files/are/')
>> convert.snp.ped(ped='hapmap3_r2_b36_fwd.CEU.qc.poly.ped',
>> map='hapmap3_r2_b36_fwd.CEU.qc.poly.map', out='ceu.out')
>> hap3data <- load.gwaa.data(phenofile = "hapmap_CEU.ph", genofile = "ceu.out")
>>
>> The thing is if I look for the genotype information of a random SNP as follows:
>>
>> as.genotype(hap3data[, "rs9976865"]@gtdata)
>>
>> The output does NOT match up with what I'm seeing on the Hapmap
>> website: http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap3r2_B36/
>>
>> If I search for the SNP here the nucleotides seem to be different and
>> they are not changing in the same way (I mean one of mine might be A/C
>> and there might be an A/A on the hapmap site). From the "Reports &
>> Analysis" drop down menu I'm selecting "Download SNP genotype data"
>> and pressing "Go" to get this information.
>>
>> Any ideas what might be going wrong here?
>>
>> Thanks,
>>
>> Paul.
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com