Pathway Testing for Longitudinal Omics
Testing multiple pathways using SLaPMEG (shared latent process mixed e...
Estimating initial values for paired slapmeg based on seperate lme mod...
Testing pathways using SLaPMEG (shared latent process mixed effects mo...
Plot the estimated random effects from SLaPMEG seperated for the study...
Print objects from multslapmeg
Print objects from slapmeg
Estimating initial values for slapmeg based on seperate lme models
Simulate longitudinal data based on a shared latent process mixed effe...
Run step II via globaltest package
Testing pathways using SLaPMEG (shared latent process mixed effects mo...
Summary of slapmeg objects
Summary of slapmeg objects
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.