PMR_individual: PMR model with individual level data

In PPMR: Probabilistic Two Sample Mendelian Randomization

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)

PPMR documentation built on Aug. 9, 2019, 5:06 p.m.