This package is considered a duplicate. The official version of this package is found at:https://mitra-ep.r-universe.dev/SlaPMEG

Package: SlaPMEG 1.0.2

Mitra Ebrahimpoor

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.

Authors:Mitra Ebrahimpoor [aut, cre]

SlaPMEG_1.0.2.tar.gz
SlaPMEG_1.0.2.zip(r-4.5)SlaPMEG_1.0.2.zip(r-4.4)
SlaPMEG_1.0.2.tgz(r-4.4-any)
SlaPMEG_1.0.2.tar.gz(r-4.5-noble)SlaPMEG_1.0.2.tar.gz(r-4.4-noble)
SlaPMEG_1.0.2.tgz(r-4.4-emscripten)SlaPMEG_1.0.2.tgz(r-4.3-emscripten)
SlaPMEG.pdf |SlaPMEG.html✨
SlaPMEG/json (API)

# Install 'SlaPMEG' in R:

install.packages('SlaPMEG', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues

On CRAN:

archived packages r-universe

2.40 score 5 stars 546 downloads 5 exports 89 dependencies

Last updated 8 days agofrom:5070e21f01 (on package/SlaPMEG). Checks:5 OK. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 13 2025
R-4.5-win	OK	Jan 13 2025
R-4.5-linux	OK	Jan 13 2025
R-4.4-win	OK	Jan 13 2025
R-4.4-mac	OK	Jan 13 2025

Exports:multslapmeg pairslapmeg plotslapmeg simslapmeg slapmeg

Dependencies:abind annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob boot cachem cli codetools colorspace cpp11 crayon curl DBI doParallel fansi farver fastmap foreach generics GenomeInfoDb GenomeInfoDbData ggplot2 globaltest glue gtable httr IRanges isoband iterators jsonlite KEGGREST labeling lattice lcmm lifecycle lme4 magic magrittr marqLevAlg MASS Matrix memoise mgcv mime minqa munsell mvtnorm nlme nloptr numDeriv openssl pillar pkgconfig plogr plyr png R6 randtoolbox rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas reshape2 rlang rngWELL RSQLite S4Vectors scales stringi stringr survival sys tibble UCSC.utils utf8 vctrs viridisLite withr XML xtable XVector

Help page	Topics
Testing multiple pathways using SLaPMEG (shared latent process mixed effects model and Globaltest) for longitudinal Omics data	multslapmeg
Estimating initial values for paired slapmeg based on seperate lme models	pairsetinval
Testing pathways using SLaPMEG (shared latent process mixed effects model and Globaltest) for longitudinal Omics data based on pairwise estimation approach (a computational solution for latrge pathways)	pairslapmeg
Plot the estimated random effects from SLaPMEG seperated for the study groups	plotslapmeg
Print objects from 'multslapmeg'	print.mslapmeg
Print objects from 'slapmeg'	print.slapmeg
Estimating initial values for slapmeg based on seperate lme models	setinval
Simulate longitudinal data based on a shared latent process mixed effects model (SlaPMEG)	simslapmeg
Run step II via globaltest package	slapGT
Testing pathways using SLaPMEG (shared latent process mixed effects model and Globaltest) for longitudinal Omics data	slapmeg
Summary of 'slapmeg' objects	summary.mslapmeg
Summary of 'slapmeg' objects	summary.slapmeg

Package: SlaPMEG 1.0.2

SlaPMEG: Pathway Testing for Longitudinal Omics

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)