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| CGHcall-package | Calling aberrations for array CGH tumor profiles. |
| 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,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,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. |
| CGHcall | Calling aberrations for array CGH tumor profiles. |
| 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. |
| 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,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: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. |
| 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,cghSeg-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| make_cghRaw | Convert a dataframe or textfile to an object of class cghRaw. |
| normalize | Normalization and cellularity adjustment for arrayCGH data. |
| plot,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data. |
| plot,cghRaw,missing-method | Class to contain and describe raw or normalized array comparative genomic hybridization data. |
| plot,cghSeg,missing-method | Class to contain and describe segmented array comparative genomic hybridization data. |
| plot.summary | Visualization of aCGH profiles. |
| plot.summary,cghCall,missing-method | Class to contain and describe called array comparative genomic hybridization data. |
| postsegnormalize | Post-segmentation normalization |
| preprocess | Preprocess arrayCGH 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. |
| segmentData | Breakpoint detection for arrayCGH 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. |
| Wilting | Cervical cancer arrayCGH data |