PMR_individual {PPMR}

PMR model with individual level data

Description

Fit the probabilistic MR model with individual level data while accounting for the correlated instruments and horizontal pleiotropy in TWAS framework.

Usage

PMR_individual(yin, zin, x1in, x2in, gammain, alphain, max_iterin, epsin)

Arguments

yin

standardized exposure vector (e.g. gene expression in TWAS).

zin

standardized complex trait vector.

x1in

standardized cis-genotype matrix in eQTL data.

x2in

standardized cis-genotype matrix in GWAS data.

gammain

indicator variable for constrained PMR model, with 1 for the null model that there is no horizontal pleiotropy.

alphain

indicator variable for constrained PMR model, with 1 for the null model that there is no causal effect.

max_iterin

The maximum iteration.

epsin

The convergence tolerance of the absolute value of the difference between the nth and (n+1)th log likelihood.

Value

a list of estimates of model parameters, including the causal effect alpha, the horizontal pleiotropy effect gamma, and the two corresponding p values

Author(s)

Zhongshang Yuan, Xiang Zhou.

Examples

data(Exampleindividual)
attach(Exampleindividual)
fmH1 = PMR_individual(yin=x, zin=y, x1in=zx, x2in=zy,
                      gammain=0,alphain = 0,max_iterin =1000,epsin=1e-5)
alpha<-fmH1$alpha
gamma<-fmH1$gamma
fmH0gamma = PMR_individual(yin=x,zin= y, x1in=zx, x2in=zy,gammain=1, 
                           alphain = 0,max_iterin =1000,epsin=1e-5)
fmH0alpha = PMR_individual(yin=x, zin=y, x1in=zx, x2in=zy,gammain=0,
                           alphain = 1,max_iterin =1000, epsin=1e-5)
loglikH1=max(fmH1$loglik,na.rm=TRUE)
loglikH0gamma=max(fmH0gamma$loglik,na.rm=TRUE)
loglikH0alpha=max(fmH0alpha$loglik,na.rm=TRUE)
stat_alpha = 2 * (loglikH1 - loglikH0alpha)
pvalue_alpha = pchisq(stat_alpha,1,lower.tail=FALSE)
stat_gamma = 2 * (loglikH1 - loglikH0gamma)
pvalue_gamma = pchisq(stat_gamma,1,lower.tail=FALSE)