slapGT

Estimated random effects by either joint or pairwise approach

Dataframe with variables required for the test

data_inf

Names of random effects defined in model

rand_nam

Ynames

Name of the covariate representing the grouping by the phenotype

grouping

Estimation method for the random effects which is either joint or pairwise

Emethod

Globaltest is used to test the association between phenotype variable and
estimated random effects from step I.

A self-contained hypothesis is tested for a given pathway of longitudinal omics. 'SlaPMEG' is a two-step procedure. First, a shared latent process mixed model is fitted over the longitudinal measures of omics in a pathway. This shared model allows deviation from the shared process at subject level (a random intercept, slope, or both per subject) and also at omic level (a random effect per omic). These random effects summarize the longitudinal trend of the observations which can be used to test for group differences using 'Globaltest' in the second step. If the pathway is large or the shared effect is small, the package fits a series of pairwise models and estimates the shared random effects based on them.

slapGT: Run step II via globaltest package

Description

Usage

Arguments

Value