[R] SNPRelate: Plink conversion

[Bert Gunter]

Doesn't this belong on Bioconductor rather than here?

-- Bert

On Fri, Nov 8, 2013 at 6:04 AM, Danica Fabrigar <danica_714 at hotmail.com> wrote:
> Hi,
>
> Following my earlier posts about having problems performing a PCA, I have
> worked out what the problem is. The problem lies within the PLINK to gds
> conversion.
>
> It seems as though the SNPs are imported as "samples" and in turn, the
> samples are recognised as SNPs:
>
>>snpsgdsSummary("chr2L")
> Some values of snp.position are invalid (should be > 0)!
> Some values of snp.chromosome are invalid (should be finite and >=1)!
> Some of snp.allele are not standard! E.g, 2/-9
> The file name: chr2L
> The total number of samples: 2638506
> The total number of SNPs: 67
> SNP genotypes are stored in SNP-major mode.
> The number of valid samples: 2638506
> The number of valid SNPs: 0
>
>
> Anyone have any ideas on how to fix this?
>
> Thanks,
> Danica
>         [[alternative HTML version deleted]]
>
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

(650) 467-7374