# CGHbase: Base functions and classes for arrayCGH data analysis.

## Documentation for package ‘CGHbase’ version 1.34.0

- DESCRIPTION file.

## Help Pages

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.