prefilterColocCandidates: Perform a quick pre-filtering between QTLs and GWAS hits to...

In kauralasoo/seqUtils:

Description

Perform a quick pre-filtering between QTLs and GWAS hits to reduce the number of coloc tests

Usage

prefilterColocCandidates(qtl_min_pvalues, gwas_prefix, gwas_variant_info,
  fdr_thresh = 0.1, overlap_dist = 1e+05, gwas_thresh = 1e-05)

Arguments

qtl_min_pvalues	List of data frames with QTL lead pvalues. Each data frame must contain gene_id, snp_id and p_fdr and should not contain other columns.
gwas_prefix	Prefix of the GWAS summarystats file
gwas_variant_info	QTL variant information in GWAS coordinates.
fdr_thresh	Minimal QTL FDR threshold
overlap_dist	Max distance between GWAS and QTL variants.
gwas_thresh	Minimal GWAS p-value threshold

Value

List of data.frames with phenotype_ids and snp_ids to be tested with coloc.

kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.