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

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.

AuthorSadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew Beck [aut], Sheida Nabavi [aut]
Date of publicationNone
MaintainerSadhika Malladi <contact@sadhikamalladi.com> and Daniel Schmolze <emd@schmolze.com>
LicenseMIT + file LICENSE
Version2.4.0

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Functions

calculate_cvm Man page
calculate_cvm_gene Man page
calculate_emd Man page
calculate_emd_gene Man page
calculate_ks Man page
calculate_ks_gene Man page
CVMomics Man page
EMDomics Man page
emdomics-package Man page
KSomics Man page
plot_cvm_density Man page
plot_cvmnull Man page
plot_cvmperms Man page
plot_emd_density Man page
plot_emdnull Man page
plot_emdperms Man page
plot_ks_density Man page
plot_ksnull Man page
plot_ksperms Man page

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