top_snps_pval_ld2_new: Rank SNPs by pval, prune for LD

Description Usage Arguments

View source: R/top_snps_pval_ld2_newformat.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_new(ld_files, snp_info_rds, snps, pval_cols = c(),
  pval_thresh = Inf, r2_thresh = 0.01,
  cores = parallel::detectCores() - 1)

Arguments

ld_files

List of h5 files containing pairwise ld. One for each chromosome.

snp_info_rds

RDS file with snp info

snps

List of snps

pval_thresh

Maximum pvalue

r2_thresh

r^2 threshold for pruning

cores

Number of cores to use

pvals

Vector of pvalues (optional)


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