CONSTANd
This is the development version of CONSTANd; for the stable release version, see CONSTANd.
Data normalization by matrix raking
Bioconductor version: Development (3.24)
Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.
Author: Joris Van Houtven [aut, trl], Geert Jan Bex [trl], Dirk Valkenborg [aut, cre]
Maintainer: Dirk Valkenborg <dirk.valkenborg at uhasselt.be>
citation("CONSTANd")):
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("CONSTANd")
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("CONSTANd")| CONSTANd | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Cheminformatics, DifferentialExpression, Genetics, MassSpectrometry, Normalization, Preprocessing, Proteomics, Software, Transcriptomics |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | file LICENSE |
| Depends | R (>= 4.1) |
| Imports | |
| System Requirements | |
| URL | qcquan.net/constand |
| Bug Reports | https://github.com/PDiracDelta/CONSTANd/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, 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 | CONSTANd_1.21.0.tar.gz |
| Windows Binary (x86_64) | CONSTANd_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | CONSTANd_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | CONSTANd_1.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CONSTANd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CONSTANd |
| Bioc Package Browser | https://code.bioconductor.org/browse/CONSTANd/ |
| Package Short Url | https://bioconductor.org/packages/CONSTANd/ |
| Package Downloads Report | Download Stats |