README.md

In stop-pre16/lmerSeq: Wrappers for Fitting Linear Mixed Models to RNA-Seq Data

lmerSeq: An R package for fitting linear mixed models to RNA-Seq data

This is the repo for the lmerSeq R package, which has the wrapper functions to run analyses of transformed RNA-Seq counts from experiments with repeated measures or other designs where correlation between samples/observations needs to be accounted for by using linear mixed models.

Installation

The lmerSeq package can easily be installed from github using devtools. Dependencies can be installed from CRAN. - First, the pbapply, lmerTest, dplyr, lme4, magrittr, gtools, nlme, numDeriv, devtools, and lavaSearch2 packages should be installed from CRAN:

install.packages(pkgs = c('pbapply', 'lmerTest', 'dplyr', 'devtools', 'magrittr', 'gtools', 'nlme', 'numDeriv', 'lavaSearch2'))

• Next, the lmerSeq package can be installed using devtools:

devtools::install_github("stop-pre16/lmerSeq", build_vignettes = T)

Tutorials

Tutorials are available in the Tutorials directory of the repository. The following tutorials are available: - Detailed tutorial for lmerSeq analysis of a simulated dataset with detailed explanation of each function - Simple analysis of a publicly available dataset using random effects - Generalized least squares models and using compound symmetric and unstructured correlation structures

In addition, a detailed vignette with an example analysis, can be viewed in R:

vignette("lmerseq-vignette")

stop-pre16/lmerSeq documentation built on July 27, 2022, 9:08 a.m.