GMD: Generalized Minimum Distance of distributions
Version 0.3.3

GMD is a package for non-parametric distance measurement between two discrete frequency distributions.

AuthorXiaobei Zhao [aut, cre, cph], Albin Sandelin [aut]
Date of publication2016-12-27 15:28:19
MaintainerXiaobei Zhao <xiaobei@binf.ku.dk>
LicenseGPL (>= 2)
Version0.3.3
URL http://CRAN.R-project.org/package=GMD
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GMD")

Getting started

Package overview

Popular man pages

cage: CAGE Data: Transcription Start Site Distributions (TSSDs) by...
chipseq: ChIP-seq data: ChIP-seq Enrichment around TSSs
css: Clustering Sum-of-Squares for clustering evaluation
ghist: Generalized Histogram Computation
mhist.summary: Bin-wise summary of histograms
plot.gmdp: Plot function for class gmdp
ts2df: Convert time series to data frame
See all...

All man pages Function index File listing

Man pages

bedgraph.to.depth: Convert a BedGraph fiel to a vector of depth-like signals
cage: CAGE Data: Transcription Start Site Distributions (TSSDs) by...
chipseq: ChIP-seq data: ChIP-seq Enrichment around TSSs
css: Clustering Sum-of-Squares for clustering evaluation
elbow: The "Elbow" Method for Clustering Evaluation
equalize.list: Make members of a list equal size
gdist: Generalized Distance Matrix Computation
get.sep: Get row or column lines of separation for heatmap.3
ghist: Generalized Histogram Computation
gmdm: Generalized Minimum Distance Matrix
gmdp: Generalized Minimum Distance between a pair of distributions
GMD-package: The Package for Generalized Minimum Distance (GMD)...
heatmap.3: Enhanced Heatmap Representation with Dendrogram and Partition
legend: Add Legends to Plots
mhist.summary: Bin-wise summary of histograms
plot.gmdm: S3 method for class 'gmdm'
plot.gmdp: Plot function for class gmdp
plot.mhist: S3 method for class 'mhist'.
ts2df: Convert time series to data frame

Functions

GMD Man page
GMD-package Man page
PairwiseDistanceMatrixToVariance Source code
as.ghist Man page Source code
as.mhist Man page Source code
bedgraph.to.depth Man page Source code
brewer.pal.Dark2 Source code
bssByDistanceMatrix Source code
cage Man page
cagel Man page
call.FUN Source code
chipseq Man page
chipseq_hCD4T Man page
chipseq_mES Man page
count.observation Source code
css Man page Source code
css.hclust Man page Source code
css.hclustM Source code
css.hclustS Source code
elbow Man page Source code
elbow.batch Man page Source code
equalize.list Man page Source code
file_path_as_absolute Source code
gbreaks Man page Source code
gdist Man page Source code
get.sep Man page Source code
ghist Man page Source code
gmd Source code
gmd0 Source code
gmdm Man page Source code
gmdm2dist Man page Source code
gmdm_dist Man page Source code
gmdp Man page Source code
heatmap.3 Man page Source code
is.dist Man page Source code
is.ghist Man page Source code
is.mhist Man page Source code
legend Man page Source code
mdpa Source code
mhist Man page
mhist.summary Man page Source code
mhist2matrix Man page Source code
normalize.vector Source code
nvalid Source code
plot.elbow Man page Source code
plot.gmdm Man page Source code
plot.gmdp Man page Source code
plot.mhist Man page Source code
plot.mhist.summary Man page Source code
plot.text Source code
print.gmdm Man page Source code
print.gmdp Man page Source code
resolveBin Source code
resolveHist Source code
retrieveDistanceMatrix Source code
s.gmd Source code
s.gmdm Source code
s.gmdp Source code
s.grouped Source code
scale.data Source code
scale.range Source code
scale.x Source code
setTextContrastColor Source code
summary.gmdp Man page Source code
totwssByDistanceMatrix Source code
ts2df Man page Source code
tssByDistanceMatrix Source code
wordwrap Source code
wssByDistanceMatrix Source code

Files

inst
inst/CITATION
inst/tests
inst/tests/GMD-demo.R
inst/extdata
inst/extdata/hg19
inst/extdata/hg19/H3K36me3.BedGraph.gz
inst/extdata/hg19/H3K27me3.BedGraph.gz
inst/extdata/hg19/H3K9me3.BedGraph.gz
inst/extdata/hg19/H3K4me2.BedGraph.gz
inst/extdata/hg19/H3K4me1.BedGraph.gz
inst/extdata/hg19/H3K4me3.BedGraph.gz
inst/doc
inst/doc/GMD-data-processing.Rnw
inst/doc/GMD-vignette.pdf
inst/doc/GMD-vignette.Rnw
inst/doc/GMD-data-processing.pdf
inst/doc/GMD-vignette.R
inst/doc/GMD-data-processing.R
src
src/base.h
src/gmd.h
src/gmd.c
NAMESPACE
demo
demo/00Index
demo/GMD-demo.R
NEWS
data
data/cage.RData
data/chipseq_hCD4T.RData
data/chipseq_mES.RData
data/cagel.RData
R
R/GMD-data.R
R/ghist.R
R/heatmap3.R
R/GMD-package.R
R/css.R
R/GMD-internal.R
R/gmdp.R
R/util.R
R/gdist.R
R/gmdm.R
R/imports.R
vignettes
vignettes/GMD-data-processing.Rnw
vignettes/bioinfo.sty
vignettes/fig
vignettes/fig/GMD-fig-case-nottem-01.pdf
vignettes/fig/GMD-fig-example-ghist-02.pdf
vignettes/fig/GMD-fig-example-ghist-01b.pdf
vignettes/fig/GMD-fig-example-GMD-01.pdf
vignettes/fig/GMD-fig-example-ghist-01.pdf
vignettes/fig/GMD-fig-case-chipseq-01.pdf
vignettes/fig/GMD-fig-case-chipseq-02.pdf
vignettes/fig/GMD-fig-example-heatmap3b-01.pdf
vignettes/fig/hg19-RPS13-histone.pdf
vignettes/fig/GMD-fig-example-css-01.pdf
vignettes/fig/GMD-fig-example-gclust-01.pdf
vignettes/fig/GMD-fig-example-heatmap3a-01.pdf
vignettes/fig/GMD-fig-case-iris-01.pdf
vignettes/fig/GMD-fig-example-gdist-01.pdf
vignettes/fig/GMD-fig-case-cage-02.pdf
vignettes/fig/GMD-fig-case-cage-01.pdf
vignettes/R
vignettes/R/example-gdist.R
vignettes/R/example-GMD.R
vignettes/R/example-ghist.R
vignettes/R/example-heatmap3b.R
vignettes/R/hello-GMD.R
vignettes/R/case-nottem.R
vignettes/R/example-css.R
vignettes/R/case-chipseq.R
vignettes/R/example-heatmap3a.R
vignettes/R/case-cage.R
vignettes/R/case-iris.R
vignettes/GMD-vignette.Rnw
vignettes/Xvignette.sty
vignettes/GMD.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/GMD-package.Rd
man/gmdp.Rd
man/heatmap.3.Rd
man/legend.Rd
man/css.Rd
man/mhist.summary.Rd
man/bedgraph.to.depth.Rd
man/ts2df.Rd
man/chipseq.Rd
man/elbow.Rd
man/plot.mhist.Rd
man/plot.gmdm.Rd
man/cage.Rd
man/gmdm.Rd
man/gdist.Rd
man/get.sep.Rd
man/plot.gmdp.Rd
man/ghist.Rd
man/equalize.list.Rd
.Rinstignore
GMD documentation built on May 19, 2017, 7:45 a.m.

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