Dear all, I´m working with Y chromosome SNP array data in vcf files. I´m trying to create genlight objects in R to perform PCA but when opened the file with vcfR package I realized that the haploid genotypes in format GT (which should be coded as 0 for reference allele and 1 for alternate) are coded as 0/0 and 1/1 respectively, as they were diploids. I read in other posts that error is pretty common with chip datasets, but I couldn´t find any suggestion to change the ploidy level in R, nor even reading in R packages manuals. Can someone please suggest any way to correct the ploidy level of my dataset? I´m pretty new in bioinformatic but I´m trying to learn to work with R. Nevertheless, plink approaches are also welcome! Any help will be really appreciated!
