# CGHbase: Base functions and classes for arrayCGH data analysis.

## Documentation for package ‘CGHbase’ version 1.2.0

## Help Pages

CGHbase-package | CGHbase: Base functions and classes for arrayCGH data analysis.
avedist | Retrieve regions information from cghRegions object.
avedist,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
bpend | Retrieve feature position data from cgh objects.
bpend,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
bpend,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
bpend,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
bpend,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
bpstart | Retrieve feature position data from cgh objects.
bpstart,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
bpstart,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
bpstart,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
bpstart,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
calls | Retrieve copynumber data from cgh objects.
calls,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
calls<- | Retrieve copynumber data from cgh objects.
calls<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
CGHbase | CGHbase: Base functions and classes for arrayCGH data analysis.
cghCall | Class to contain and describe called array comparative genomic hybridization data.
cghCall-class | Class to contain and describe called array comparative genomic hybridization data.
cghRaw | Class to contain and describe raw or normalized array comparative genomic hybridization data.
cghRaw-class | Class to contain and describe raw or normalized array comparative genomic hybridization data.
cghRegions | Class to contain and describe array comparative genomic hybridization regions data.
cghRegions-class | Class to contain and describe array comparative genomic hybridization regions data.
cghSeg | Class to contain and describe segmented array comparative genomic hybridization data.
cghSeg-class | Class to contain and describe segmented array comparative genomic hybridization data.
chromosomes | Retrieve feature position data from cgh objects.
chromosomes,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
chromosomes,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
chromosomes,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
chromosomes,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
class:cghCall | Class to contain and describe called array comparative genomic hybridization data.
class:cghRaw | Class to contain and describe raw or normalized array comparative genomic hybridization data.
class:cghRegions | Class to contain and describe array comparative genomic hybridization regions data.
class:cghSeg | Class to contain and describe segmented array comparative genomic hybridization data.
copynumber | Retrieve copynumber data from cgh objects.
copynumber,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
copynumber,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
copynumber,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
copynumber<- | Retrieve copynumber data from cgh objects.
copynumber<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
copynumber<-,cghRaw,matrix-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
copynumber<-,cghSeg,matrix-method | Class to contain and describe segmented array comparative genomic hybridization data.
frequencyPlot | Visualization of aCGH regions.
frequencyPlot,cghRegions,missing-method | Class to contain and describe array comparative genomic hybridization regions data.
initialize,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
initialize,cghRaw-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
initialize,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
initialize,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
nclone | Retrieve regions information from cghRegions object.
nclone,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
plot.cghCall | Plot aCGH data.
plot.cghCall,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data.
plot.cghRaw | Plot aCGH data.
plot.cghRaw,cghRaw,missing-method | Class to contain and describe raw or normalized array comparative genomic hybridization data.
plot.cghRegions | Plot aCGH data.
plot.cghRegions,cghRegions,missing-method | Class to contain and describe array comparative genomic hybridization regions data.
plot.cghSeg | Plot aCGH data.
plot.cghSeg,cghSeg,missing-method | Class to contain and describe segmented array comparative genomic hybridization data.
probamp | Retrieve call probabilities from a cghCall object.
probamp,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
probamp<- | Retrieve call probabilities from a cghCall object.
probamp<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
probgain | Retrieve call probabilities from a cghCall object.
probgain,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
probgain<- | Retrieve call probabilities from a cghCall object.
probgain<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
probloss | Retrieve call probabilities from a cghCall object.
probloss,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
probloss<- | Retrieve call probabilities from a cghCall object.
probloss<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
probnorm | Retrieve call probabilities from a cghCall object.
probnorm,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
probnorm<- | Retrieve call probabilities from a cghCall object.
probnorm<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
regions | Retrieve regions data from cghRegions object.
regions,cghRegions-method | Class to contain and describe array comparative genomic hybridization regions data.
regions<- | Retrieve regions data from cghRegions object.
regions<-,cghRegions,matrix-method | Class to contain and describe array comparative genomic hybridization regions data.
segmented | Retrieve copynumber data from cgh objects.
segmented,cghCall-method | Class to contain and describe called array comparative genomic hybridization data.
segmented,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data.
segmented<- | Retrieve copynumber data from cgh objects.
segmented<-,cghCall,matrix-method | Class to contain and describe called array comparative genomic hybridization data.
segmented<-,cghSeg,matrix-method | Class to contain and describe segmented array comparative genomic hybridization data.
summaryPlot | Visualization of aCGH profiles.
summaryPlot,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data.
WiltingCalled | Cervical cancer arrayCGH data called with CGHcall
WiltingData | Cervical cancer arrayCGH data
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 CGHregions
WiltingSeg | Segmented log2 ratios from cervical cancer arrayCGH data.