This is the released version of PLSDAbatch; for the devel version, see PLSDAbatch.
PLSDA-batchBioconductor version: Release (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 âPLSDA-batchâ. 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: 0000-0002-7067-9093 , Kim-Anh Le Cao [aut]
Maintainer: Yiwen (Eva) Wang <anjiwangyiwen at gmail.com>
Citation (from within R, entercitation("PLSDAbatch")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PLSDAbatch")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PLSDAbatch")Follow Installation instructions to use this package in your R session.
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