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SNPRelate: Plink conversion
4 messages · Bert Gunter, Danica Fabrigar, Hermann Norpois
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
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Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374
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