Registration and Call for Abstracts Open for Bioc2024

PLSDAbatch

This is the development version of PLSDAbatch; to use it, please install the devel version of Bioconductor.

PLSDA-batch


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.3
In Bioconductor since BioC 3.19 (R-4.4)
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/
See More
Suggests knitr, rmarkdown, testthat, badger
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package PLSDAbatch_0.99.3.tar.gz
Windows Binary PLSDAbatch_0.99.3.zip
macOS Binary (x86_64) PLSDAbatch_0.99.3.tgz
macOS Binary (arm64) PLSDAbatch_0.99.3.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/
Package Downloads Report Download Stats