Computate Generalized Minimum Distance (GMD) between discrete distributions and clustering tools
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 SumofSquares 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.rproject.org")
## Sometimes the offical repository might not be up to date, then ## you may install it from a downloaded source file; please replace ## '<currentversion>' with actual version numbers: Note that as ## new versions are release, the '<currentversion>' changes. install.packages(pkgs="GMD_<currentversion>.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
NULL
Xiaobei Zhao and Albin Sandelin
Maintainer: Xiaobei Zhao xiaobei (at) binf.ku.dk
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.
gmdp
, gmdm
, cage
, chipseq
, ghist
,
gdist
, css
, elbow
, heatmap.3
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  ## 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("GMDdemo") # run the demo
## view GMD Description
packageDescription("GMD")
## view GMD vignette
vignette("GMDvignette",package="GMD")
## End(Not run)

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