PLSDAbatch

PLSDA-batch


Bioconductor version: Release (3.19)

A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.

Author: Yiwen (Eva) Wang [aut, cre] , Kim-Anh Le Cao [aut]

Maintainer: Yiwen (Eva) Wang <anjiwangyiwen at gmail.com>

Citation (from within R, enter citation("PLSDAbatch")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PLSDAbatch")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PLSDAbatch")
PLSDA-batch Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Classification, DimensionReduction, Microbiome, Normalization, PrincipalComponent, Software, StatisticalMethod, Visualization
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment
System Requirements
URL https://github.com/EvaYiwenWang/PLSDAbatch
Bug Reports https://github.com/EvaYiwenWang/PLSDAbatch/issues/
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Suggests knitr, rmarkdown, testthat, badger
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PLSDAbatch_1.0.0.tar.gz
Windows Binary (x86_64) PLSDAbatch_1.0.0.zip
macOS Binary (x86_64) PLSDAbatch_1.0.0.tgz
macOS Binary (arm64) PLSDAbatch_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PLSDAbatch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PLSDAbatch
Bioc Package Browser https://code.bioconductor.org/browse/PLSDAbatch/
Package Short Url https://bioconductor.org/packages/PLSDAbatch/
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