Package: PLSDAbatch
Type: Package
Title: PLSDA-batch
Version: 2.1.0
Authors@R: 
    c(person(given = "Yiwen (Eva)", family = "Wang", role = c("aut", "cre"), email = "anjiwangyiwen@gmail.com", comment=c(ORCID="0000-0002-7067-9093")),
      person(given = "Kim-Anh", family = "Le Cao", role = "aut", email = "kimanh.lecao@unimelb.edu.au"))
Description: 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. 
License: GPL-3
Depends: R (>= 4.5.0)
Imports: ggplot2, ggpubr, grid, gridExtra, lmerTest, mixOmics,
        performance, scales, stats, Rdpack
Suggests: SummarizedExperiment, TreeSummarizedExperiment, vegan, knitr,
        rmarkdown, BiocStyle, testthat, badger, pheatmap, Biobase
biocViews: StatisticalMethod, DimensionReduction, PrincipalComponent,
        Classification, Microbiome, BatchEffect, Normalization,
        Visualization
VignetteBuilder: knitr
RdMacros: Rdpack
RoxygenNote: 7.3.3
Encoding: UTF-8
URL: https://github.com/EvaYiwenWang/PLSDAbatch
BugReports: https://github.com/EvaYiwenWang/PLSDAbatch/issues/
git_url: https://git.bioconductor.org/packages/PLSDAbatch
git_branch: devel
git_last_commit: 5f1e835
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-05-18
NeedsCompilation: no
Packaged: 2026-05-18 23:03:05 UTC; biocbuild
Author: Yiwen (Eva) Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7067-9093>),
  Kim-Anh Le Cao [aut]
Maintainer: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Built: R 4.6.0; ; 2026-05-19 05:03:24 UTC; unix
