CGHbase: Base functions and classes for arrayCGH data analysis.

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Documentation for package ‘CGHbase’ version 1.68.0

• DESCRIPTION file.

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