chroGPS: chroGPS: visualizing the epigenome
Version 1.24.0

We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds.

Browse man pages Browse package API and functions Browse package files

AuthorOscar Reina, David Rossell
Bioconductor views Clustering Visualization
Date of publicationNone
MaintainerOscar Reina <oscar.reina@irbbarcelona.org>
LicenseGPL (>=2.14)
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chroGPS")

Man pages

addVar: Plot vector of a quantitative variable over a MDS map.
adjustPeaks: Adjust peak width so that samples obtained under different...
boostMDS: Improve goodness-of-fit of a given MDS solution in terms of...
clusGPS: Computation of cluster density estimates for cluster contour...
clusGPS-class: Class '"clusGPS"'
distGPS: Compute matrix with pairwise distances between objects....
distGPS-class: Class '"distGPS"'
domainDist: Overview of intra and inter-domain distances.
geneSetGPS: Highlight point (gene) position over a Multi-dimensional...
getURL: Retrieve file from URL.
gff2RDList: Retrieve binding site information from GFF3 files.
gps2xgmml: Export an 'mds' object to Cytoscape .xgmml format
mds: Metric and non-metric Multidimensional Scaling for a distGPS...
mds-class: Class '"mds"'
mergeClusters: Unsupervised cluster merging based on their observed overlap...
procrustesAdj: Use Procrustes to adjust an MDS map containing samples...
profileClusters: Compute enrichment/depletion ratio for the observed...
s2: Sample binding site and related data from S2 and BG3 cell...
splitDistGPS-class: Class '"splitDistGPS"'

Functions

addVar Man page Source code
adjustPeaks Man page
adjustPeaks,GRangesList-method Man page
adjustPeaks-methods Man page
as.matrix,distGPS-method Man page
avgdistpair Source code
avgdistpair.old Source code
boostMDS Man page Source code
changewidth Source code
chisqdist Source code
chisqdist2 Source code
clusGPS Man page
clusGPS,distGPS,mds-method Man page
clusGPS-class Man page
clusGPS-method Man page
clusGPS-methods Man page
clusNames Man page
clusNames,clusGPS-method Man page
clusOverlap Source code
clusterID Man page
clusterID,clusGPS-method Man page
combs Source code
contour2dDP Man page Source code
d Man page
d2 Man page
d3 Man page
distGPS Man page
distGPS,GRangesList-method Man page
distGPS,data.frame-method Man page
distGPS,matrix-method Man page
distGPS-class Man page
distGPS-methods Man page
domainDist Man page Source code
geneSetGPS Man page
geneSetGPS,data.frame,mds,character-method Man page
geneSetGPS,matrix,mds,character-method Man page
geneSetGPS-methods Man page
getAttributeField Source code
getPoints Man page
getPoints,mds-method Man page
getR2 Man page
getR2,mds-method Man page
getStress Man page
getStress,mds-method Man page
getURL Man page Source code
getmodEncodeBS Source code
gff2RDList Man page Source code
gffRead Source code
gps2xgmml Man page
gps2xgmml,mds,ANY-method Man page
gps2xgmml,mds-method Man page
hclust-class Man page
is.adj Man page
is.adj,mds-method Man page
mds Man page
mds,distGPS,mds-method Man page
mds,distGPS,missing-method Man page
mds,splitDistGPS,missing-method Man page
mds-class Man page
mds-methods Man page
mergeClusters Man page
mergeClusters,clusGPS-method Man page
mergeClusters,list-method Man page
mergeClusters-methods Man page
mergeMDS Source code
normCoords Source code
pden.adjust Source code
plot,clusGPS,ANY-method Man page
plot,clusGPS-method Man page
plot,mds,ANY-method Man page
plot,mds-method Man page
plotContour Man page Source code
preCalcGrid Source code
premergeClusters Source code
procrustes Source code
procrustesAdj Man page
procrustesAdj,mds,distGPS-method Man page
procrustesAdj-methods Man page
profileClusters Man page Source code
rdldist Source code
realtanipair Source code
realtanipair.old Source code
s2 Man page
s2.tab Man page
s2.wt Man page
s2Seq Man page
s2SeqNames Man page
s2names Man page
show,clusGPS-method Man page
show,distGPS-method Man page
show,mds-method Man page
show,splitDistGPS-method Man page
splidDistGPS-class Man page
splitDistGPS,data.frame-method Man page
splitDistGPS,distGPS-method Man page
splitDistGPS,matrix-method Man page
splitDistGPS-class Man page
splitMDS Source code
stress Source code
tabClusters Man page
tabClusters,clusGPS-method Man page
toydists Man page
uniqueCount Man page Source code
xgmml2d Source code
xgmml3d Source code

Files

DESCRIPTION
NAMESPACE
R
R/adjustPeaks.R
R/clusGPS.R
R/distGPS.R
R/domainDist.R
R/geneSetGPS.R
R/getmodEncode.R
R/gff2RDList.R
R/gps2xgmml.R
R/mds-class.R
R/mds.R
R/procrustesAdj.R
build
build/vignette.rds
data
data/datalist
data/s2.RData
data/s2Seq.RData
data/toydists.RData
inst
inst/NEWS
inst/doc
inst/doc/chroGPS.R
inst/doc/chroGPS.Rnw
inst/doc/chroGPS.pdf
man
man/addVar.Rd
man/adjustPeaks.Rd
man/boostMDS.Rd
man/clusGPS-class.Rd
man/clusGPS.Rd
man/distGPS-class.Rd
man/distGPS.Rd
man/domainDist.Rd
man/geneSetGPS.Rd
man/getURL.Rd
man/gff2RDList.Rd
man/gps2xgmml.Rd
man/mds-class.Rd
man/mds.Rd
man/mergeClusters.Rd
man/procrustesAdj.Rd
man/profileClusters.Rd
man/s2.Rd
man/splitDistGPS-class.Rd
vignettes
vignettes/chroGPS-cyto.png
vignettes/chroGPS-cyto3d.png
vignettes/chroGPS.Rnw
vignettes/mds-2d-3d.png
vignettes/mds3d_1.png
vignettes/references.bib
chroGPS documentation built on May 20, 2017, 9:24 p.m.