EMDomics

DOI: 10.18129/B9.bioc.EMDomics    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see EMDomics.

Earth Mover's Distance for Differential Analysis of Genomics Data

Bioconductor version: 3.8

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.

Author: Sadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi [aut]

Maintainer: Sadhika Malladi <contact at sadhikamalladi.com> and Daniel Schmolze <emd at schmolze.com>

Installation

To install this package, start R (version "3.5") and enter:

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

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("EMDomics")

 

HTML	R Script	EMDomics Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, Microarray, Software
Version	2.12.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	MIT + file LICENSE
Depends	R (>= 3.2.1)
Imports	emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	EMDomics_2.12.0.tar.gz
Windows Binary	EMDomics_2.12.0.zip
Mac OS X 10.11 (El Capitan)	EMDomics_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EMDomics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EMDomics
Package Short Url	http://bioconductor.org/packages/EMDomics/
Package Downloads Report	Download Stats