plhood: Pseudo-likelihood for a set of observations of Z_d and Z_a

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

Description

Pseudo-likelihood for a set of observations of Z_d and Z_a

Usage

plhood(Z, pars, weights = rep(1, dim(Z)[1]), sumlog = TRUE, C = 1)

Arguments

Z	an n x 2 array; Z[i,1], Z[i,2] are the Z_d and Z_a scores respectively for the ith SNP
pars	vector containing initial values of pi0,pi1,tau,sigma1,sigma2,rho.
weights	SNP weights to adjust for LD; output from LDAK procedure
sumlog	set to TRUE to return the (weighted) sum of log pseudo-likelihoods for each datapoint; FALSE to return a vector of pseudo-likelihoods for each datapoint.
C	scaling factor for adjustment

Value

value of pseudo- log likelihood of all observations (if sumlog==TRUE) or vector of n pseudo-likelihoods (if sumlog==FALSE)

Author(s)

James Liley

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