robustLossFixtau: Calculate the robustified profile likelihood function

In jingshuw/GRAPPLE-beta-: R Package for MR Framework GRAPPLE

Calculate the robustified profile likelihood function

Description

Calculate the robustified profile likelihood function

Usage

robustLossFixtau(
  data = NULL,
  b_exp = NULL,
  b_out = NULL,
  se_exp = NULL,
  se_out = NULL,
  cor.mat = NULL,
  loss.function = c("tukey", "huber", "l2"),
  k.findmodes = switch(loss.function[1], l2 = NA, huber = 1.345, tukey = 3)
)

Arguments

data	A data frame containing the information of the selected genetic instruments. One can simply take the data element from the output of function getInput, or provide their own data frame. The required columns include SNP for the SNP rsID, the columns gamma_exp1 to gamma_expk for the estimated effect sizes of the SNPs on risk factors 1 to k, the columns se_exp1 to se_expk for their standard deviations, the columns gamma_out1 to gamma_outm for the estimated effect sizes of the SNPs on diseases 1 to m,the columns se_out1 to se_outm for their standard deviations.
cor.mat	Either NULL or a k + 1 by k + 1 symmetric matrix. The shared correlation matrix for (b_exp[j], b_out[j]) across SNP j. Used only when input.list is NULL and the default value is NULL, for the identity matrix.
loss.function	Loss function used, one of "tukey", "huber" or "l2". Default is "tukey", which is robust to outlier SNPs with large pleiotropic effects
k.findmodes	Tuning parameters of the loss function, for loss "l2", it is NA, for loss "huber", default is 1.345 and for loss "tukey", default is 3.

Value

The robustified profile likelihood function

jingshuw/GRAPPLE-beta- documentation built on March 29, 2024, 1:26 p.m.