PLSDAbatch
This is the development version of PLSDAbatch; for the stable release version, see PLSDAbatch.
PLSDA-batch
Bioconductor version: Development (3.24)
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.
Author: Yiwen (Eva) Wang [aut, cre]
, Kim-Anh Le Cao [aut]
Maintainer: Yiwen (Eva) Wang <anjiwangyiwen at gmail.com>
citation("PLSDAbatch")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("PLSDAbatch")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PLSDAbatch")| PLSDA-batch Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Classification, DimensionReduction, Microbiome, Normalization, PrincipalComponent, Software, StatisticalMethod, Visualization |
| Version | 2.1.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | ggplot2, ggpubr, grid, gridExtra, lmerTest, mixOmics, performance, scales, stats, Rdpack |
| System Requirements | |
| URL | https://github.com/EvaYiwenWang/PLSDAbatch |
| Bug Reports | https://github.com/EvaYiwenWang/PLSDAbatch/issues/ |
See More
| Suggests | SummarizedExperiment, TreeSummarizedExperiment, vegan, knitr, rmarkdown, BiocStyle, testthat, badger, pheatmap, Biobase |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PLSDAbatch_2.1.1.tar.gz |
| Windows Binary (x86_64) | PLSDAbatch_2.1.1.zip |
| macOS Binary (big-sur-x86_64) | PLSDAbatch_2.1.1.tgz |
| macOS Binary (sonoma-arm64) | PLSDAbatch_2.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PLSDAbatch |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PLSDAbatch |
| Bioc Package Browser | https://code.bioconductor.org/browse/PLSDAbatch/ |
| Package Short Url | https://bioconductor.org/packages/PLSDAbatch/ |
| Package Downloads Report | Download Stats |