PLSDAbatch

A multivariate and non-parametric batch effect correction framework based on Projection to Latent Structures Discriminant Analysis for microbiome data. This repository contains the R package hosted on Bioconductor.

Maintainer

Yiwen (Eva) Wang

Installation

(macOS users only: Ensure you have installed XQuartz first.)

Make sure you have the latest R version and the latest BiocManager package installed following these instructions.

## install BiocManager if not installed
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

Ensure the following returns TRUE, or follow the guidelines provided by the output.

BiocManager::valid()

a) Latest Bioconductor Release (not now, wait for Bioconductor release)

You can install PLSDAbatch using the following code:

BiocManager::install('PLSDAbatch')

b) GitHub Version

Install the GitHub version with:

# without vignette
BiocManager::install("EvaYiwenWang/PLSDAbatch") 

# with vignette
devtools::install_github("https://github.com/EvaYiwenWang/PLSDAbatch", build_vignettes = T)

Functions preview

library(PLSDAbatch)

## names
ls('package:PLSDAbatch')

## names and details
lsf.str('package:PLSDAbatch')

Vignette View

browseVignettes("PLSDAbatch")

Bug reports/Feature requests

Open a new issue.

Reference

Wang, Y., & Lê Cao, K. A. (2023). PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data. Briefings in Bioinformatics, 24(2), bbac622.

https://academic.oup.com/bib/article/24/2/bbac622/6991121 (The mentioned simulations and analyses in the paper are separately stored here.)

What’s New

April 2023

• submitted to Bioconductor.