CGHbase: Base functions and classes for arrayCGH data analysis.

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Documentation for package ‘CGHbase’ version 1.32.0

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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.