mist_logit: mist_logit

In mcanouil/MiSTr: Mixed effects Score Test for continuous outcomes

mist_logit

Description

mist_logit

Arguments

y	[numeric] A numeric vector of the continuous outcome variables. Missing values are not allowed.
X	[numeric] A numeric matrix of covariates with rows for individuals and columns for covariates. If there is no covariate, it does not need to be specified
G	[numeric] A numeric genotype matrix with rows for individuals and columns for SNPs. Each SNP should be coded as 0, 1, and 2 for AA, Aa, aa, where A is a major allele and a is a minor allele. Missing genotypes are not allowed.
Z	[numeric] a numeric matrix of second level covariates for variant characteristics. Each row corresponds to a variant and each column corresponds to a variant characteristic. If there is no second level covariates, a vector of 1 should be used.
method	[character] A method to compute the p-value and the default value is "liu". Method "davies" represents an exact method that computes the p-value by inverting the characteristic function of the mixture chisq. Method "liu" represents an approximation method that matches the first 3 moments.
weight.beta	[numeric] A numeric vector of parameters of beta function which is the weight for scorestatistics. The default value is NULL, i.e. no weight. Default weight value could be c(1, 25).
maf	[numeric] A numeric vector of MAF (minor allele frequency) for each SNP.

Value

data.frame

mcanouil/MiSTr documentation built on April 7, 2023, 10:48 a.m.