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# 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](mailto:wangyiwen@caas.cn)
## Installation
(**macOS users only:** Ensure you have installed
[XQuartz](https://www.xquartz.org/) first.)
Make sure you have the latest R version and the latest `BiocManager`
package installed following [these
instructions](https://www.bioconductor.org/install/).
``` r
## 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.
``` r
BiocManager::valid()
```
#### a) Latest `Bioconductor` Release (not now, wait for Bioconductor release)
You can install `PLSDAbatch` using the following code:
``` r
BiocManager::install('PLSDAbatch')
```
#### b) `GitHub` Version
Install the GitHub version with:
``` r
# without vignette
BiocManager::install("EvaYiwenWang/PLSDAbatch")
# with vignette
devtools::install_github("https://github.com/EvaYiwenWang/PLSDAbatch", build_vignettes = T)
```
## Functions preview
``` r
library(PLSDAbatch)
## names
ls('package:PLSDAbatch')
## names and details
lsf.str('package:PLSDAbatch')
```
## Vignette View
``` r
browseVignettes("PLSDAbatch")
```
## Bug reports/Feature requests
[Open a new issue](https://github.com/EvaYiwenWang/PLSDAbatch/issues).
## 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](https://evayiwenwang.github.io/PLSDAbatch_workflow/).)
## What’s New
#### April 2023
- submitted to Bioconductor.
#### September 2024
- fixed bugs: the clash of functions from dependencies.
