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.
1 2 3 | 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 |
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