inst/R_cli/plink_to_snpstats.R

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

# plink_to_snpstats <- function(vcf_subset,
#                               LD_reference,
#                               superpopulation,
#                               select_snps,
#                               locus_dir,
#                               nThread = 1,
#                               verbose = TRUE) {
#     vcf.gz.path <- filter_vcf_cli(
#         vcf_subset = vcf_subset,
#         LD_reference = LD_reference,
#         superpopulation = superpopulation,
#         remove_tmp = TRUE,
#         verbose = verbose
#     )
#     bed_bim_fam <- vcf_to_bed_cli(
#         vcf.gz.subset = vcf.gz.path,
#         locus_dir = locus_dir,
#         verbose = verbose
#     )
#     # dir.create(LD_folder, showWarnings = FALSE, recursive = TRUE)
#     # select_snps= arg needed bc otherwise read.plink() sometimes complains of
#     ## duplicate RSID rownames. Also need to check whether these
#     # SNPs exist in the plink files.
#     ## (snpStats doesn't have very good error handling for these cases).
#     select_snps <- snpstats_ensure_nonduplicates(
#         select_snps = select_snps,
#         bim_path = bed_bim_fam$bim,
#         nThread = nThread,
#         verbose = verbose
#     )
#     # Only need to give bed path (infers bin/fam paths)
#     ss <- snpStats::read.plink(
#         bed = bed_bim_fam$bed,
#         select.snps = select_snps
#     )
#     return(ss)
# }