top_snps_pval_ld2: Rank SNPs by pval, prune for LD

Description Usage Arguments

View source: R/top_snps_pval_ld2.R

Description

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.

Usage

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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)

Arguments

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


jean997/sherlockAsh documentation built on Oct. 6, 2018, 3:14 p.m.