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

[Paul Geeleher]

Hi,

I'm loading HapMap III data from here:
ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/

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.

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