CGHcall-package |
Calling aberrations for array CGH tumor profiles. |
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,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,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. |
CGHcall |
Calling aberrations for array CGH tumor profiles. |
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. |
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,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: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. |
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,cghSeg-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. |
normalize |
Normalization and cellularity adjustment for arrayCGH data. |
plot,cghCall,missing-method |
Class to contain and describe called array comparative genomic hybridization data. |
plot,cghRaw,missing-method |
Class to contain and describe raw or normalized array comparative genomic hybridization data. |
plot,cghSeg,missing-method |
Class to contain and describe segmented array comparative genomic hybridization data. |
plot.summary |
Visualization of aCGH profiles. |
plot.summary,cghCall,missing-method |
Class to contain and describe called array comparative genomic hybridization data. |
preprocess |
Preprocess arrayCGH 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. |
segmentData |
Breakpoint detection for arrayCGH data. |
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. |
Wilting |
Cervical cancer arrayCGH data |