load_gwas: This function loads and checks set of univariate P values for...

In ollyburren/rCOGS: Computes gene prioritisation scores based on promoter capture Hi-C data

Description

This function loads and checks set of univariate P values for a given trait and adds posterior probabilities for each SNP to be causal using Wakefield's aBF

Usage

load_gwas(f, maf.DT, ld.gr, n.cases, n.controls, plink = FALSE)

Arguments

f	character scalar representing GWAS file to load, tab delimited with three columns chr,pos and p
maf.DT	a data.table of reference MAFs created by load_ref_maf
ld.gr	a GenomicRanges object of LD regions created by load_ld_regions
n.cases	a scalar for the number of GWAS cases - this should equal sample size in the case of a quantitative trait
n.controls	a scalar for the number of GWAS controls - this should be omitted in the case of a quantitative trait
plink	a boolean as to whether input format is PLINK rather than the cannonical type described above.

Value

a data.table of annotated GWAS variants suitable for COGS analysis

ollyburren/rCOGS documentation built on Aug. 5, 2020, 2:13 p.m.