PLSDAbatch

A new multivariate and non-parametric batch effect correction method based on Projection to Latent Structures Discriminant Analysis for microbiome data.

pkgdown web page

The web page includes all the functions and vignettes within the package.

Link: https://evayiwenwang.github.io/PLSDAbatch/

Installation with github

Installation without vignettes

devtools::install_github("https://github.com/EvaYiwenWang/PLSDAbatch")

Installation with vignettes

First, we need to install the packages necessary for vignettes.

# CRAN
cran.pkgs <- c('pheatmap', 'vegan', 'ruv', 'UpSetR', 'gplots', 
               'ggplot2', 'gridExtra', 'performance')
               
for(c in seq_len(length(cran.pkgs))){
if (!requireNamespace(cran.pkgs[c], quietly = TRUE))
    install.packages(cran.pkgs[c])
}
    
# Bioconductor
bioc.pkgs <- c('mixOmics', 'sva', 'limma', 'Biobase', 'metagenomeSeq')

for(b in seq_len(length(bioc.pkgs))){
if (!requireNamespace(bioc.pkgs[b], quietly = TRUE))
    BiocManager::install(bioc.pkgs[b])
}

Then, we are able to install PLSDAbatch with vignettes using the following command line.

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

Installation with source code

https://github.com/EvaYiwenWang/PLSDAbatch-source-code

Reference

Wang, Y., & Lê Cao, K. A. (2020). A multivariate method to correct for batch effects in microbiome data. bioRxiv. https://www.biorxiv.org/content/10.1101/2020.10.27.358283v1