Package: PLSDAbatch
Type: Package
Title: PLSDA-batch
Version: 1.7.0
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/
git_url: https://git.bioconductor.org/packages/PLSDAbatch
git_branch: devel
git_last_commit: 744879e
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
