| GMD-package {GMD} | R Documentation |
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 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
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
## 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)