The Package for Generalized Minimum Distance (GMD) Computation

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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

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## 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)