# 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.

- 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

## 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 |