ld_prune_pval_format3: Rank SNPs by pval, prune for LD
In jean997/sherlockAsh: CAUSE: Causal Analysis Using Summary Effect Estimates

Description Usage Arguments

Selects a set of top SNP based on p-value that are in minimal LD. Performs the same function as top_snps_pval_ld but with different input format.

ld_prune_pval_format3(ld_files, snp_info_files, snps, pval_cols = NA,
  data_snp_col = "SNP", snp_info_snp_col = "SNP",
  rowsnp_col = "rowsnp", colsnp_col = "colsnp", pval_thresh = Inf,
  r2_thresh = 0.01, cores = parallel::detectCores() - 1)

`ld_files`	List of file prefixes for LD files. One for each chromosome
`snps`	List of snps
`pval_thresh`	Maximum pvalue
`r2_thresh`	r^2 threshold for pruning
`cores`	Number of cores to use
`snp_info_rds`	List of RDS files with snp info. One for each chromosome.
`pvals`	Vector of pvalues (optional)