Entry: CGHcall-package
Aliases: CGHcall-package
Keywords: package
Description: Calling aberrations for array CGH tumor profiles.
URL: ../../../library/CGHcall/html/CGHcall-package.html

Entry: CGHcall
Aliases: CGHcall
Keywords: misc
Description: Calling aberrations for array CGH tumor profiles.
URL: ../../../library/CGHcall/html/CGHcall.html

Entry: Wilting
Aliases: Wilting
Keywords: datasets
Description: Cervical cancer arrayCGH data
URL: ../../../library/CGHcall/html/Wilting.html

Entry: chromosomes
Aliases: chromosomes bpstart bpend
Keywords: manip
Description: Retrieve feature position data from cgh objects.
URL: ../../../library/CGHcall/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,missing-method plot.summary,cghCall,missing-method
Keywords: classes
Description: Class to contain and describe called array comparative genomic hybridization data.
URL: ../../../library/CGHcall/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,missing-method
Keywords: classes
Description: Class to contain and describe raw or normalized array comparative genomic hybridization data.
URL: ../../../library/CGHcall/html/class.cghRaw.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,missing-method
Keywords: classes
Description: Class to contain and describe segmented array comparative genomic hybridization data.
URL: ../../../library/CGHcall/html/class.cghSeg.html

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

Entry: make_cghRaw
Aliases: make_cghRaw
Keywords: misc
Description: Convert a dataframe or textfile to an object of class cghRaw.
URL: ../../../library/CGHcall/html/make_cghRaw.html

Entry: normalize
Aliases: normalize
Keywords: misc
Description: Normalization and cellularity adjustment for arrayCGH data.
URL: ../../../library/CGHcall/html/normalize.html

Entry: plot.summary
Aliases: plot.summary
Keywords: misc
Description: Visualization of aCGH profiles.
URL: ../../../library/CGHcall/html/plot.summary.html

Entry: preprocess
Aliases: preprocess
Keywords: misc
Description: Preprocess arrayCGH data
URL: ../../../library/CGHcall/html/preprocess.html

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

Entry: segmentData
Aliases: segmentData
Keywords: misc
Description: Breakpoint detection for arrayCGH data.
URL: ../../../library/CGHcall/html/segmentData.html
