BatchVaria
This is the development version of BatchVaria; to use it, please install the devel version of Bioconductor.
Variance-Aware Evaluation of Batch Correction
Bioconductor version: Development (3.24)
Evaluates batch correction in omics data by quantifying how a correction redistributes variance, not only whether it removes it. Records correction and variance-decomposition provenance in the metadata of an ordinary SummarizedExperiment, and harmonises both the batch correction methods and the variance-profiling engines behind documented contracts, so that either set can be extended without modifying the package. Variance fractions are compositional, so removing variance associated with one term inflates the fraction attributed to every other. Each decomposition is therefore recorded alongside the total variance it is relative to and the share an unbalanced design cannot attribute to any single term, which is what distinguishes a correction that removed unwanted variation from one that merely removed variation.
Author: Nicholas Moir [aut, cre]
Maintainer: Nicholas Moir <nicholas.moir at ed.ac.uk>
citation("BatchVaria")):
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("BatchVaria")
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("BatchVaria")| BatchVaria Quickstart: Evaluating Batch Correction Performance | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DataRepresentation, GeneExpression, Normalization, QualityControl, RNASeq, Sequencing, Software, StatisticalMethod, Transcriptomics, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0), SummarizedExperiment |
| Imports | S4Vectors, rlang, methods, variancePartition, stats, ggplot2, FNN, reformulas, sva, tidyr, tidyselect, dplyr, grid |
| System Requirements | |
| URL | https://github.com/cmpmolonc/BatchVaria |
| Bug Reports | https://github.com/cmpmolonc/BatchVaria/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, limma |
| 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 | BatchVaria_0.99.2.tar.gz |
| Windows Binary (x86_64) | BatchVaria_0.99.2.zip |
| macOS Binary (big-sur-x86_64) | BatchVaria_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | BatchVaria_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BatchVaria |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BatchVaria |
| Bioc Package Browser | https://code.bioconductor.org/browse/BatchVaria/ |
| Package Short Url | https://bioconductor.org/packages/BatchVaria/ |
| Package Downloads Report | Download Stats |