R: The Package for Generalized Minimum Distance (GMD)...

GMD-package {GMD} | R Documentation

## The Package for Generalized Minimum Distance (GMD) Computation

### Description

Computate Generalized Minimum Distance (GMD) between discrete distributions and clustering tools

### Details

Package: | GMD
Type: | Package
License: | GPL (>= 2)

This package contains:
1) modules and functions for GMD computation, with GMD algorithm implemented in C to interface with R.
2) related clustering and visualization tools for distributions.

An overview of functions

Function | Description
`ghist` | Generalized Histogram Computation and Visualization
`gdist` | Generalized Distance Matrix Computation
`css` | Computing Clustering Sum-of-Squares and
| evaluating the clustering by the “elbow” method
`heatmap.3` | Enhanced Heatmap Representation with Dendrogram and Partition
`gmdp` | Computation of GMD on a pair of histograms
`gmdm` | Computation of GMD Matrix on a set of histograms

## To install from online repositories (e.g. CRAN) install.packages(pkgs="GMD", repos="http://cran.r-project.org")

## Sometimes the offical repository might not be up to date, then ## you may install it from a downloaded source file; please replace ## '<current-version>' with actual version numbers: Note that as ## new versions are release, the '<current-version>' changes. install.packages(pkgs="GMD_<current-version>.tar.gz", repos=NULL)

## Load the package and get a complete list of functions, use library(GMD) ls("package:GMD")

## help documantation of the package help(GMD) # this page

### Value

`NULL`

### Author(s)

Xiaobei Zhao and Albin Sandelin

Maintainer: Xiaobei Zhao xiaobei (at) binf.ku.dk

### References

Zhao et al (2011), "Systematic Clustering of Transcription Start Site Landscapes", PLoS ONE 6(8): e23409.
http://dx.plos.org/10.1371/journal.pone.0023409

See `citation("GMD")` for BibTeX entries for LaTeX users.

### See Also

`gmdp`, `gmdm`, `cage`, `chipseq`, `ghist`, `gdist`, `css`, `elbow`, `heatmap.3`

### Examples

    ## Not run:
    require(GMD)        # load GMD
    help(GMD)           # a help document of GMD
    data(package="GMD") # a list of datasets available in GMD
    ls("package:GMD")   # a list of functions available in GMD
    help(package="GMD") # help documentation on GMD
    citation("GMD")     # citation for publications
    demo("GMD-demo")    # run the demo

    ## view GMD Description
    packageDescription("GMD")

    ## view GMD vignette
    vignette("GMD-vignette",package="GMD")

    ## End(Not run)

[Package GMD version 0.3.3 Index]