mr_cML_DP_Overlap: MRcML method for overlapping samples with Data Perturbation

In xue-hr/MRcML: Mendelian randomization method with constrained maximum likelihood.

MRcML method for overlapping samples with Data Perturbation

Description

This is the main function of MRcML method for overlapping samples with data perturbation.

Usage

mr_cML_DP_Overlap(
  b_exp,
  b_out,
  se_exp,
  se_out,
  K_vec = 0:(length(b_exp) - 2),
  random_start = 0,
  random_start_pert = 0,
  maxit = 100,
  num_pert = 100,
  random_seed = 0,
  n,
  rho = 0
)

Arguments

b_exp	Vector of estimated effects for exposure.
b_out	Vector or estimated effects for outcome.
se_exp	Vector of standard errors for exposure.
se_out	Vector of standard errors for outcome.
K_vec	Sets of candidate K's, the constraint parameter representing number of invalid IVs.
random_start	Number of random start points for cML, default is 0.
random_start_pert	Number of random start points for cML with data perturbation, default is 0.
maxit	Maximum number of iterations for each optimization.
num_pert	Number of perturbation, default is 200.
random_seed	Random seed, an integer. Default is 0, which does not set random seed; user could specify a positive integer as random seed to get replicable results.
n	Sample size.
rho	Correlation between GWAS summary statistics due to overlapping samples.

Value

A list contains full results of cML methods. MA_BIC_theta, MA_BIC_se, MA_BIC_p: Estimate of theta, its standard error and p-value from cML-MA-BIC. Similarly for BIC_theta, BIC_se, BIC_p from cML-BIC; for MA_BIC_DP_theta, MA_BIC_DP_se, MA_BIC_DP_p from cML-MA-BIC-DP; for BIC_DP_theta, BIC_DP_se, BIC_DP_p from cML-BIC-DP. BIC_invalid is the set of invalid IVs selected by cML-BIC.

xue-hr/MRcML documentation built on Aug. 25, 2024, 4:24 p.m.