CONSTANd

DOI: 10.18129/B9.bioc.CONSTANd    

This is the development version of CONSTANd; to use it, please install the devel version of Bioconductor.

Data normalization by matrix raking

Bioconductor version: Development (3.13)

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 (from within R, enter citation("CONSTANd")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

 

HTML R Script CONSTANd
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Cheminformatics, DifferentialExpression, Genetics, MassSpectrometry, Normalization, Preprocessing, Proteomics, Software, Transcriptomics
Version 0.99.6
In Bioconductor since BioC 3.13 (R-4.1)
License file LICENSE
Depends R (>= 4.1)
Imports
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma
SystemRequirements
Enhances
URL qcquan.net/constand
BugReports https://github.com/PDiracDelta/CONSTANd/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CONSTANd_0.99.6.tar.gz
Windows Binary CONSTANd_0.99.6.zip
macOS 10.13 (High Sierra) CONSTANd_0.99.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/CONSTANd
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CONSTANd
Package Short Url https://bioconductor.org/packages/CONSTANd/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: