getpx: getpx

In jamesliley/subtest: Test whether two putative subgroups of a disease phenotype show evidence of differential genetic basis.

Description

Given some set of parameters in pars, compute the posterior likelihood of membership of each group for a set of SNP Z scores

Usage

getpx(Z, pars)

Arguments

Z	n x 2 matrix of Z scores; Z[,1]=Z_d, Z[,2]=Z_a
pars	parameters of full model; in order, pi0, pi1, tau, sigma_1, sigma_2, rho
i	get posterior probability of this group; if null, get posterior probability of all groups.

Value

n x 3 matrix; element [i,j] is probability of SNP i being in group j.

Author(s)

James Liley

Examples

nn=100000
Z=abs(rbind(rmnorm(0.8*nn,varcov=diag(2)), rmnorm(0.15*nn,varcov=rbind(c(1,0),c(0,2^2))), rmnorm(0.05*nn,varcov=rbind(c(3^2,2),c(2,4^2)))));
pars=c(0.8,0.15,3,2,4,2)
gp=getpx(Z,pars)
plotZ(Z,rlim=2,col=rgb(gp))

jamesliley/subtest documentation built on May 18, 2019, 11:21 a.m.