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

[Martin Morgan]

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

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