Entry: CGHbase-package
Aliases: CGHbase-package CGHbase
Keywords: package
Description: CGHbase: Base functions and classes for arrayCGH data analysis.
URL: ../../../library/CGHbase/html/CGHbase-package.html

Entry: WiltingCalled
Aliases: WiltingCalled
Keywords: datasets
Description: Cervical cancer arrayCGH data called with CGHcall
URL: ../../../library/CGHbase/html/WiltingCalled.html

Entry: WiltingData
Aliases: WiltingData
Keywords: datasets
Description: Cervical cancer arrayCGH data
URL: ../../../library/CGHbase/html/WiltingData.html

Entry: WiltingNorm
Aliases: WiltingNorm
Keywords: datasets
Description: Normalized log2 ratios from cervical cancer arrayCGH data.
URL: ../../../library/CGHbase/html/WiltingNorm.html

Entry: WiltingRaw
Aliases: WiltingRaw
Keywords: datasets
Description: Raw log2 ratios from cervical cancer arrayCGH data.
URL: ../../../library/CGHbase/html/WiltingRaw.html

Entry: WiltingRegions
Aliases: WiltingRegions
Keywords: datasets
Description: Regions of cervical cancer arrayCGH data as defined by CGHregions
URL: ../../../library/CGHbase/html/WiltingRegions.html

Entry: WiltingSeg
Aliases: WiltingSeg
Keywords: datasets
Description: Segmented log2 ratios from cervical cancer arrayCGH data.
URL: ../../../library/CGHbase/html/WiltingSeg.html

Entry: avedist
Aliases: avedist nclone
Keywords: manip
Description: Retrieve regions information from cghRegions object.
URL: ../../../library/CGHbase/html/avedist.html

Entry: chromosomes
Aliases: chromosomes bpstart bpend
Keywords: manip
Description: Retrieve feature position data from cgh objects.
URL: ../../../library/CGHbase/html/chromosomes.html

Entry: cghCall
Aliases: class:cghCall cghCall cghCall-class copynumber,cghCall-method copynumber<-,cghCall,matrix-method segmented,cghCall-method segmented<-,cghCall,matrix-method calls,cghCall-method calls<-,cghCall,matrix-method probloss,cghCall-method probloss<-,cghCall,matrix-method probnorm,cghCall-method probnorm<-,cghCall,matrix-method probgain,cghCall-method probgain<-,cghCall,matrix-method probamp,cghCall-method probamp<-,cghCall,matrix-method chromosomes,cghCall-method bpstart,cghCall-method bpend,cghCall-method initialize,cghCall-method plot.cghCall,cghCall,missing-method summaryPlot,cghCall,missing-method
Keywords: classes
Description: Class to contain and describe called array comparative genomic hybridization data.
URL: ../../../library/CGHbase/html/class.cghCall.html

Entry: cghRaw
Aliases: class:cghRaw cghRaw cghRaw-class copynumber,cghRaw-method copynumber<-,cghRaw,matrix-method chromosomes,cghRaw-method bpstart,cghRaw-method bpend,cghRaw-method initialize,cghRaw-method plot.cghRaw,cghRaw,missing-method
Keywords: classes
Description: Class to contain and describe raw or normalized array comparative genomic hybridization data.
URL: ../../../library/CGHbase/html/class.cghRaw.html

Entry: cghRegions
Aliases: class:cghRegions cghRegions cghRegions-class regions,cghRegions-method regions<-,cghRegions,matrix-method chromosomes,cghRegions-method bpstart,cghRegions-method bpend,cghRegions-method nclone,cghRegions-method avedist,cghRegions-method initialize,cghRegions-method plot.cghRegions,cghRegions,missing-method frequencyPlot,cghRegions,missing-method
Keywords: classes
Description: Class to contain and describe array comparative genomic hybridization regions data.
URL: ../../../library/CGHbase/html/class.cghRegions.html

Entry: cghSeg
Aliases: class:cghSeg cghSeg cghSeg-class copynumber,cghSeg-method copynumber<-,cghSeg,matrix-method segmented,cghSeg-method segmented<-,cghSeg,matrix-method chromosomes,cghSeg-method bpstart,cghSeg-method bpend,cghSeg-method initialize,cghSeg-method plot.cghSeg,cghSeg,missing-method
Keywords: classes
Description: Class to contain and describe segmented array comparative genomic hybridization data.
URL: ../../../library/CGHbase/html/class.cghSeg.html

Entry: copynumber
Aliases: copynumber copynumber<- segmented segmented<- calls calls<-
Keywords: manip
Description: Retrieve copynumber data from cgh objects.
URL: ../../../library/CGHbase/html/copynumber.html

Entry: frequencyPlot
Aliases: frequencyPlot
Keywords: misc
Description: Visualization of aCGH regions.
URL: ../../../library/CGHbase/html/frequencyPlot.html

Entry: plot.cghRaw
Aliases: plot.cghRaw plot.cghSeg plot.cghCall plot.cghRegions
Keywords: 
Description: Plot aCGH data.
URL: ../../../library/CGHbase/html/plot.html

Entry: probloss
Aliases: probloss probnorm probgain probamp probloss<- probnorm<- probgain<- probamp<-
Keywords: manip
Description: Retrieve call probabilities from a cghCall object.
URL: ../../../library/CGHbase/html/probloss.html

Entry: regions
Aliases: regions regions<-
Keywords: manip
Description: Retrieve regions data from cghRegions object.
URL: ../../../library/CGHbase/html/regions.html

Entry: summaryPlot
Aliases: summaryPlot
Keywords: misc
Description: Visualization of aCGH profiles.
URL: ../../../library/CGHbase/html/summaryPlot.html
