CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.
Version 1.36.0

Contains functions and classes that are needed by arrayCGH packages.

Browse man pages Browse package API and functions Browse package files

AuthorSjoerd Vosse, Mark van de Wiel
Bioconductor views CopyNumberVariation Infrastructure Microarray
Date of publicationNone
MaintainerMark van de Wiel <mark.vdwiel@vumc.nl>
LicenseGPL
Version1.36.0
URL https://github.com/tgac-vumc/CGHbase
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CGHbase")

Man pages

avedist: Retrieve regions information from cghRegions object.
CGHbase-package: CGHbase: Base functions and classes for arrayCGH data...
chromosomes: Retrieve feature position data from cgh objects.
class.cghCall: Class to contain and describe called array comparative...
class.cghRaw: Class to contain and describe raw or normalized array...
class.cghRegions: Class to contain and describe array comparative genomic...
class.cghSeg: Class to contain and describe segmented array comparative...
copynumber: Retrieve copynumber data from cgh objects.
frequencyPlot: Visualization of aCGH regions.
frequencyPlotCalls: Visualization of aCGH profiles.
make_cghRaw: Convert a dataframe or textfile to an object of class cghRaw.
plot: Plot aCGH data.
probloss: Retrieve call probabilities from a cghCall object.
regions: Retrieve regions data from cghRegions object.
summaryPlot: Visualization of aCGH profiles.
Wilting: Cervical cancer arrayCGH data
WiltingCalled: Cervical cancer arrayCGH data called with CGHcall
WiltingNorm: Normalized log2 ratios from cervical cancer arrayCGH data.
WiltingRaw: Raw log2 ratios from cervical cancer arrayCGH data.
WiltingRegions: Regions of cervical cancer arrayCGH data as defined by...
WiltingSeg: Segmented log2 ratios from cervical cancer arrayCGH data.

Functions

CGHbase Man page
CGHbase-package Man page
Wilting Man page
WiltingCalled Man page
WiltingNorm Man page
WiltingRaw Man page
WiltingRegions Man page
WiltingSeg Man page
avedist Man page
avedist,cghRegions-method Man page
bpend Man page
bpend,cghCall-method Man page
bpend,cghRaw-method Man page
bpend,cghRegions-method Man page
bpend,cghSeg-method Man page
bpstart Man page
bpstart,cghCall-method Man page
bpstart,cghRaw-method Man page
bpstart,cghRegions-method Man page
bpstart,cghSeg-method Man page
calls Man page
calls,cghCall-method Man page
calls<- Man page
calls<-,cghCall,matrix-method Man page
cghCall Man page
cghCall-class Man page
cghRaw Man page
cghRaw-class Man page
cghRegions Man page
cghRegions-class Man page
cghSeg Man page
cghSeg-class Man page
chromosomes Man page
chromosomes,cghCall-method Man page
chromosomes,cghRaw-method Man page
chromosomes,cghRegions-method Man page
chromosomes,cghSeg-method Man page
class:cghCall Man page
class:cghRaw Man page
class:cghRegions Man page
class:cghSeg Man page
convertChromosomeToArm Source code
copynumber Man page
copynumber,cghCall-method Man page
copynumber,cghRaw-method Man page
copynumber,cghSeg-method Man page
copynumber<- Man page
copynumber<-,cghCall,matrix-method Man page
copynumber<-,cghRaw,matrix-method Man page
copynumber<-,cghSeg,matrix-method Man page
featureDataRequiredColumns Source code
frequencyPlot Man page
frequencyPlot,cghRegions,missing-method Man page
frequencyPlotCalls Man page Source code
frequencyPlotCalls,cghCall,missing-method Man page
getCentromere Source code
getChromosomeLengths Source code
initialize,cghCall-method Man page
initialize,cghRaw-method Man page
initialize,cghRegions-method Man page
initialize,cghSeg-method Man page
makeEmptyFeatureData Source code
makeEmptyFeatureDataForRegions Source code
makeSegments Source code
make_cghRaw Man page Source code
nclone Man page
nclone,cghRegions-method Man page
plot,cghCall,missing-method Man page
plot,cghRaw,missing-method Man page
plot,cghSeg,missing-method Man page
plot.cghCall Man page
plot.cghRaw Man page
plot.cghRegions Man page
plot.cghRegions,cghRegions,missing-method Man page
plot.cghSeg Man page
plot.summary,cghCall,missing-method Man page
probamp Man page
probamp,cghCall-method Man page
probamp<- Man page
probamp<-,cghCall,matrix-method Man page
probdloss Man page
probdloss,cghCall-method Man page
probdloss<- Man page
probdloss<-,cghCall,matrix-method Man page
probgain Man page
probgain,cghCall-method Man page
probgain<- Man page
probgain<-,cghCall,matrix-method Man page
probloss Man page
probloss,cghCall-method Man page
probloss<- Man page
probloss<-,cghCall,matrix-method Man page
probnorm Man page
probnorm,cghCall-method Man page
probnorm<- Man page
probnorm<-,cghCall,matrix-method Man page
regions Man page
regions,cghRegions-method Man page
regions<- Man page
regions<-,cghRegions,matrix-method Man page
segmented Man page
segmented,cghCall-method Man page
segmented,cghSeg-method Man page
segmented<- Man page
segmented<-,cghCall,matrix-method Man page
segmented<-,cghSeg,matrix-method Man page
setFeatureData Source code
summaryPlot Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/allGeneric.R
R/classes.R
R/methods-cghCall.R
R/methods-cghRaw.R
R/methods-cghRegions.R
R/methods-cghSeg.R
R/private.R
R/tools.R
data
data/Wilting.txt
data/WiltingCalled.rda
data/WiltingNorm.rda
data/WiltingRaw.rda
data/WiltingRegions.rda
data/WiltingSeg.rda
data/datalist
man
man/CGHbase-package.Rd
man/Wilting.Rd
man/WiltingCalled.Rd
man/WiltingNorm.Rd
man/WiltingRaw.Rd
man/WiltingRegions.Rd
man/WiltingSeg.Rd
man/avedist.Rd
man/chromosomes.Rd
man/class.cghCall.Rd
man/class.cghRaw.Rd
man/class.cghRegions.Rd
man/class.cghSeg.Rd
man/copynumber.Rd
man/frequencyPlot.Rd
man/frequencyPlotCalls.Rd
man/make_cghRaw.Rd
man/plot.Rd
man/probloss.Rd
man/regions.Rd
man/summaryPlot.Rd
CGHbase documentation built on May 20, 2017, 9:45 p.m.