PLSDAbatch
This is the development version of PLSDAbatch; for the stable release version, see PLSDAbatch.
PLSDA-batch
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Yiwen (Eva) Wang <anjiwangyiwen at gmail.com>
citation("PLSDAbatch")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Classification, DimensionReduction, Microbiome, Normalization, PrincipalComponent, Software, StatisticalMethod, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |