top_snps_pval_ld2: 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.

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top_snps_pval_ld2(pairwise_ld, ld_chunk_files, pvals, snp_list, ld_chunks,
  pval_thresh = Inf, r2_thresh = 0.01,
  cores = parallel::detectCores() - 1)

`pairwise_ld`	Should have four columns (rowsnp, colsnp r^2, chunk)
`ld_chunk_files`	List of RDS files containing pairwise ld. Provide either pairwise_ld or ld_chunk_files.
`pvals`	Vector of pvalues (optional)
`snp_list`	List of snps
`ld_chunks`	chunk number for each SNP. If chunk has missing values, those SNPs are assumed not in LD with any other SNPs.
`pval_thresh`	Maximum pvalue
`max_snps`	Maximum number of SNPs to retain
`ld_thresh`	Maximum pairwise correlation between SNPs