Re: [R] SNPRelate: Plink conversion
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 __ 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.
Re: [R] SNPRelate: Plink conversion
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.
Re: [R] SNPRelate: Plink conversion
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.
