ld_prune_pval_format3: Rank SNPs by pval, prune for LD

Description Usage Arguments

View source: R/ld_prune_pval_format3.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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ld_prune_pval_format3(ld_files, snp_info_files, snps, pval_cols = NA,
  data_snp_col = "SNP", snp_info_snp_col = "SNP",
  rowsnp_col = "rowsnp", colsnp_col = "colsnp", pval_thresh = Inf,
  r2_thresh = 0.01, cores = parallel::detectCores() - 1)

Arguments

ld_files

List of file prefixes for LD files. One for each chromosome

snps

List of snps

pval_thresh

Maximum pvalue

r2_thresh

r^2 threshold for pruning

cores

Number of cores to use

snp_info_rds

List of RDS files with snp info. One for each chromosome.

pvals

Vector of pvalues (optional)


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