GMD (version 0.3.3)

GMD-package: The Package for Generalized Minimum Distance (GMD) Computation

Description

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

Value

NULL

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 ## '' with actual version numbers: Note that as ## new versions are release, the '' changes. install.packages(pkgs="GMD_.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

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)