search for: snpsgdssummary

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...