Package: PLSDAbatch
Type: Package
Title: PLSDA-batch
Version: 1.6.0
Authors@R: 
    c(person(given = "Yiwen", family = "Wang", middle = "(Eva)", 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 (>= 4.3.0)
Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr,
        lmerTest, performance, grid, stats, pheatmap, vegan, Biobase,
        BiocStyle, TreeSummarizedExperiment
Suggests: knitr, rmarkdown, testthat, badger
biocViews: StatisticalMethod, DimensionReduction, PrincipalComponent,
        Classification, Microbiome, BatchEffect, Normalization,
        Visualization
VignetteBuilder: knitr
RdMacros: Rdpack
RoxygenNote: 7.2.3
Encoding: UTF-8
URL: https://github.com/EvaYiwenWang/PLSDAbatch
BugReports: https://github.com/EvaYiwenWang/PLSDAbatch/issues/
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        make texlive libicu-dev libpng-dev libxml2-dev libgl1-mesa-dev
        libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:26:59 UTC
RemoteUrl: https://github.com/bioc/PLSDAbatch
RemoteRef: RELEASE_3_22
RemoteSha: 77783a72e9de563ff087d86405288a3046ce4c3a
NeedsCompilation: no
Packaged: 2026-01-24 20:48:03 UTC; root
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 4.5.2; ; 2026-01-24 20:50:27 UTC; windows
