I successfully ran LD pruning from SNPRelate package and obtained the selected SNPs IDs. I would like to create a new GDS file with only the pruned SNPs so I can use it in another software. Codes:
#read in vcf file vcf.fn <- ""C:/Users/HP/Desktop/Magic_FavoritePanel_VCF_SNPs.vcf" # reformat to create gds file snpgdsVCF2GDS(vcf.fn, "panelReformat.gds", method="biallelic.only") snpgdsSummary("panelReformat.gds") #open the GDS file genofile <- snpgdsOpen("panelReformat.gds") #Perfom LD-based SNP pruning set.seed(1000) snpset <- snpgdsLDpruning(genofile, ld.threshold=0.2) names(snpset) # Final output, get all selected snp id snpset.id <- unlist(snpset)
snpset.id is not a complete dataset; how do I extract from the original GDS file only the data set related to the selected SNP IDs and save it as GDS file? With this, I can play with the data in many ways; I can convert it back to VCF and analyze it in Tassel or STRUCTURE.
Thank you in advance