EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data
Version 2.6.0

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.

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AuthorSadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi [aut]
Bioconductor views DifferentialExpression GeneExpression Microarray Software
Date of publicationNone
MaintainerSadhika Malladi <contact@sadhikamalladi.com> and Daniel Schmolze <emd@schmolze.com>
LicenseMIT + file LICENSE
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EMDomics")

Man pages

calculate_cvm: Cramer von Mises for differential analysis of genomics data
calculate_cvm_gene: Calculate CVM score for a single gene
calculate_emd: Earth Mover's Distance for differential analysis of genomics...
calculate_emd_gene: Calculate EMD score for a single gene
calculate_ks: Calculate the Komolgorov-Smirnov test statistic and q-values...
calculate_ks_gene: Calculate KS score for a single gene
CVMomics: Create an CVMomics object
EMDomics: Create an EMDomics object
emdomics-package: Earth Mover's Distance algorithm for differential analysis of...
KSomics: Create an KSomics object
plot_cvm_density: Plot distributions and CVM score for a gene.
plot_cvmnull: Plot null distribution of permuted cvm scores vs. calculated...
plot_cvmperms: Plot histogram of CVM scores calculated via random...
plot_emd_density: Plot distributions and EMD score for a gene.
plot_emdnull: Plot null distribution of permuted EMD scores vs. calculated...
plot_emdperms: Plot histogram of EMD scores calculated via random...
plot_ks_density: Plot distributions and KS score for a gene.
plot_ksnull: Plot null distribution of permuted ks scores vs. calculated...
plot_ksperms: Plot histogram of KS scores calculated via random...

Functions

CVMomics Man page Source code
EMDomics Man page Source code
KSomics Man page Source code
calculate_cvm Man page Source code
calculate_cvm_gene Man page Source code
calculate_emd Man page Source code
calculate_emd_gene Man page Source code
calculate_ks Man page Source code
calculate_ks_gene Man page Source code
cvm_pairwise_q Source code
cvm_pairwise_table Source code
emd_gene_pairwise Source code
emd_pairwise_q Source code
emd_pairwise_table Source code
emdomics-package Man page
ks_pairwise_table Source code
plot_cvm_density Man page Source code
plot_cvmnull Man page Source code
plot_cvmperms Man page Source code
plot_emd_density Man page Source code
plot_emdnull Man page Source code
plot_emdperms Man page Source code
plot_ks_density Man page Source code
plot_ksnull Man page Source code
plot_ksperms Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/CVM.R
R/EMD.R
R/KS.R
R/plots.R
build
build/vignette.rds
inst
inst/doc
inst/doc/EMDomics.R
inst/doc/EMDomics.Rmd
inst/doc/EMDomics.html
man
man/CVMomics.Rd
man/EMDomics.Rd
man/KSomics.Rd
man/calculate_cvm.Rd
man/calculate_cvm_gene.Rd
man/calculate_emd.Rd
man/calculate_emd_gene.Rd
man/calculate_ks.Rd
man/calculate_ks_gene.Rd
man/emdomics-package.Rd
man/plot_cvm_density.Rd
man/plot_cvmnull.Rd
man/plot_cvmperms.Rd
man/plot_emd_density.Rd
man/plot_emdnull.Rd
man/plot_emdperms.Rd
man/plot_ks_density.Rd
man/plot_ksnull.Rd
man/plot_ksperms.Rd
vignettes
vignettes/EMDomics.Rmd
vignettes/EMDomics.md
vignettes/figure
EMDomics documentation built on May 20, 2017, 10:07 p.m.