plot_h: A scatter plot of the mean downweighting level against the...

In siqixu/MRCIP: MRCIP: A robust Mendelian randomization method accounting for correlated and idiosyncratic pleiotropy

Description

This function provides a scatter plot of the mean downweighting level against the bandwidth in the kernel estimation

Usage

plot_h(data,beta=0,mu_gamma=NA,s_gamma=NA,s_alpha=NA,rho=0,h_start=0.01,h_step=0.01,tol_dw=1e-4,tol=1e-8,n_iter=1000,plot_h="TRUE")

Arguments

data	A matrix or data frame consists of four columns: the 1st(2nd) column contains the estimated genetic effects on the outcome (exposure); the 3rd (4th) column contains the estimated standard errors of the estimated genetic effects on the outcome (exposure).
beta	The initial value of the causal effect in the PRW-EM algorithm. The default value is zero
mu_gamma	The initial value for the mean of the genetic effects on the exposure in the PRW-EM algorithm. If it is missing, the sample mean of the estimated genetic effects on the exposure will be used.
s_gamma	The initial value for the standard error of the genetic effects on the exposure in the PRW-EM algorithm. If it is missing, it will be calculated based on the sample variance of the estimated genetic effects on the exposure.
s_alpha	The initial value for the standard error of the pleiotropy effects on the outcome in the PRW-EM algorithm. If it is missing, it will be calculated based on the sample variance of the estimated genetic effects on the outcome.
rho	The initial value of the correlated pleiotropy index (CPI) in the PRW-EM algorithm. The default value is zero.
h_start	The start value in the grid search for the bandwidth used in the kernel estimation. The default value is 0.01.
h_step	The step size in the grid search for the bandwidth used in the kernel estimation. The default value is 0.01.
tol_dw	The grid search for the bandwidth stops when the difference in the mean downweighting between two consecutive steps is less than tol_dw.
tol	The tolerance used in the PRW-EM algorithm. The PRW-EM algorithm stops when the difference in the weighted log-likelihood function between two consecutive iterations is less than tol. The default value is 1e-8.
n_iter	The maximum number of iterations in the PRW-EM algorithm. The default value is 1000.
plot_h	If it is "TRUE", then a plot of the mean downweighting level against the bandwidth will be produced.

Value

dw	A matrix containing two columns. The 1st column is the bandwidth used in the kernel estimation. The 2nd column is the corresponding empirical mean downweighting level given the bandwidth in the 1st column.
sel_h	The possible abrupt change in the empirical mean down-weighting level over a grid of bandwidth values. If no abrupt change is detected, it will be set to the maximum value among the grid of bandwidth values

Examples

  plot_h(data=example)

siqixu/MRCIP documentation built on Jan. 28, 2021, 9:42 a.m.