ld_prune_pval_format4: Rank SNPs by pval, prune for LD

Description Usage Arguments

View source: R/ld_prune_pval_format4.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_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)

Arguments

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)


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