Function to downsample independent SNPs to match MAF distribution of whole set.

Matches MAF distribution of independent set of SNPs to MAF distribution of whole set of SNPs to avoid MAF-based confounding.

match_ind_maf(maf, indep_index)

Arguments

maf	minor allele frequencies of (all) SNPs
indep_index	indices of independent SNPs

Value

indices of independent SNP in chosen in sample

Details

Must supply maf values from the whole data set, not just the independent SNPs.