# function to extract regions from VCF file for data simulation
subset_vcf=function(seed_number){
#
# # plot(vcf$maf)
# quantile(vcf$maf)
subsetVCF = function(vcf, var_index = NA) {
vcf2 = as.list(vcf)
s = var_index
vcf2$maf = vcf2$maf [s]
vcf2$varid = vcf2$varid [s]
vcf2$gt1 = vcf2$gt1 [s,]
vcf2$gt2 = vcf2$gt2 [s,]
vcf2$vcf = vcf2$vcf [s,]
as.environment(vcf2)
}
# str(as.list(vcf))
# # find number of variants in the vcf file
num_variants = nrow(vcf$gt1)
# num_individuals = ncol(vcf$gt1)
#
#
# select first 300 variants
set.seed(seed_number)
var_select = sample(1:num_variants,nvariants)
vcf2 = subsetVCF(vcf, var_select)
#
# str(as.list(vcf2))
# dim(vcf$gt1)
# dim(vcf2$gt1)
return(vcf2)
}
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