Package: PLSDAbatch
Type: Package
Title: PLSDA-batch
Version: 1.0.0
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: RELEASE_3_19
git_last_commit: 397c738
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 01:03:16 UTC; biocbuild
Author: Yiwen (Eva) Wang [aut, cre] (<https://orcid.org/0000-0002-7067-9093>),
  Kim-Anh Le Cao [aut]
Maintainer: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Built: R 4.4.0; ; 2024-05-02 13:17:28 UTC; windows
