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