You might try to import your data in GenABEL, use as.numeric (gtdata (data)) to get a matrix that delivers you 0,1 or 2 for each snp and id (observation) and then try prcomp.
Also check this http://gettinggeneticsdone.blogspot.de/2011/10/new-dimension-to-principal-components_27.html http://www.hsph.harvard.edu/alkes-price/software/ Hope this helps. Hermann 2013/11/8 Danica Fabrigar <danica_...@hotmail.com> > Hi Bert, > I thought it was suitable to post the question on the R mailing list first > seeing as the problem/question is related to an R package..... > > Danica > > > > > Date: Fri, 8 Nov 2013 08:14:03 -0800 > > Subject: Re: [R] SNPRelate: Plink conversion > > From: gunter.ber...@gene.com > > To: danica_...@hotmail.com > > CC: r-help@r-project.org > > > > Doesn't this belong on Bioconductor rather than here? > > > > -- Bert > > > > On Fri, Nov 8, 2013 at 6:04 AM, Danica Fabrigar <danica_...@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]] > > > > > > ______________________________________________ > > > R-help@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code. > > > > > > > > -- > > > > Bert Gunter > > Genentech Nonclinical Biostatistics > > > > (650) 467-7374 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
