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 4 5 | ld_prune_pval_format4(ld_file_lists, snp_info_files, snps, pval_col = NA,
data_snp_col = "SNP", snp_info_snp_col = "SNP",
rowsnp_col = "rowsnp", colsnp_col = "colsnp", r2_col = "r2",
pval_thresh = Inf, r2_thresh = 0.01,
cores = parallel::detectCores() - 1)
|
snps |
List of snps |
pval_thresh |
Maximum pvalue |
r2_thresh |
r^2 threshold for pruning |
cores |
Number of cores to use |
List |
of vectors of LD files |
snp_info_rds |
List of RDS files with snp info. One for each chromosome. |
pvals |
Vector of pvalues (optional) |
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