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

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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]
Date of publication
None
Maintainer
Sadhika Malladi <contact@sadhikamalladi.com> and Daniel Schmolze <emd@schmolze.com>
License
MIT + file LICENSE
Version
2.4.0

View on Bioconductor

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...

Files in this package

EMDomics/DESCRIPTION
EMDomics/LICENSE
EMDomics/NAMESPACE
EMDomics/NEWS
EMDomics/R
EMDomics/R/CVM.R
EMDomics/R/EMD.R
EMDomics/R/KS.R
EMDomics/R/plots.R
EMDomics/build
EMDomics/build/vignette.rds
EMDomics/inst
EMDomics/inst/doc
EMDomics/inst/doc/EMDomics.R
EMDomics/inst/doc/EMDomics.Rmd
EMDomics/inst/doc/EMDomics.html
EMDomics/man
EMDomics/man/CVMomics.Rd
EMDomics/man/EMDomics.Rd
EMDomics/man/KSomics.Rd
EMDomics/man/calculate_cvm.Rd
EMDomics/man/calculate_cvm_gene.Rd
EMDomics/man/calculate_emd.Rd
EMDomics/man/calculate_emd_gene.Rd
EMDomics/man/calculate_ks.Rd
EMDomics/man/calculate_ks_gene.Rd
EMDomics/man/emdomics-package.Rd
EMDomics/man/plot_cvm_density.Rd
EMDomics/man/plot_cvmnull.Rd
EMDomics/man/plot_cvmperms.Rd
EMDomics/man/plot_emd_density.Rd
EMDomics/man/plot_emdnull.Rd
EMDomics/man/plot_emdperms.Rd
EMDomics/man/plot_ks_density.Rd
EMDomics/man/plot_ksnull.Rd
EMDomics/man/plot_ksperms.Rd
EMDomics/vignettes
EMDomics/vignettes/EMDomics.Rmd
EMDomics/vignettes/EMDomics.md
EMDomics/vignettes/figure