CGHbase: Base functions and classes for arrayCGH data analysis.

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Documentation for package ‘CGHbase’ version 1.8.0

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