SlaPMEG: Pathway Testing for Longitudinal Omics

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.

Version:	1.0.2
Depends:	R (≥ 4.0.0)
Imports:	lme4 (≥ 1.1.21), lcmm (≥ 1.8.1), globaltest (≥ 5.36.0), magic (≥ 1.5.9), reshape2 (≥ 1.4.3), ggplot2 (≥ 3.2.1), mvtnorm
Published:	2024-11-05
DOI:	10.32614/CRAN.package.SlaPMEG
Author:	Mitra Ebrahimpoor [aut, cre]
Maintainer:	Mitra Ebrahimpoor <mitra.ebrahimpoor at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
Citation:	SlaPMEG citation info
Materials:	README
In views:	Omics
CRAN checks:	SlaPMEG results [issues need fixing before 2025-01-12]

Documentation:

Reference manual:

SlaPMEG.pdf

Downloads:

Package source:	SlaPMEG_1.0.2.tar.gz
Windows binaries:	r-devel: SlaPMEG_1.0.2.zip, r-release: SlaPMEG_1.0.2.zip, r-oldrel: SlaPMEG_1.0.2.zip
macOS binaries:	r-release (arm64): SlaPMEG_1.0.2.tgz, r-oldrel (arm64): SlaPMEG_1.0.2.tgz, r-release (x86_64): SlaPMEG_1.0.2.tgz, r-oldrel (x86_64): SlaPMEG_1.0.2.tgz
Old sources:	SlaPMEG archive

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