adjust_LD: adjust LD for variable sample size

In colocPropTest: Proportional Testing for Colocalisation Analysis

adjust LD for variable sample size

Description

adjust LD for variable sample size

Usage

adjust_LD(S, LD)

Arguments

S	coloc style dataset, with additional entries n0 and n1 which are *vectors* giving the number of cases and controls genotyped at each SNP
LD	matrix of LD, with dimnames given by snps in S$snp

Value

adjusted LD matrix

Examples

library(coloc)

data(coloc_test_data)
attach(coloc_test_data)
LD=D1$LD
dimnames(LD)=list(D1$snp,D1$snp)
D1$type="cc"
D1$s=.5
D1$n1=D1$N * sample(c(0.25,.5),length(D1$snp), replace=TRUE)
D1$n0=rep(0.5*D1$N,length(D1$snp))
aLD=colocPropTest::adjust_LD(D1,LD)
LD[1:6,1:6]
aLD[1:6,1:6]
detach(coloc_test_data)

colocPropTest documentation built on June 24, 2024, 9:08 a.m.