CGHbase: Base functions and classes for arrayCGH data analysis.

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Documentation for package ‘CGHbase’ version 1.2.0

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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.