Calling aberrations for array CGH tumor profiles.

Documentation for package ‘CGHcall’ version 2.12.0

DESCRIPTION file.
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CGHcall-package	Calling aberrations for array CGH tumor profiles.
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 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 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.
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-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 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-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.
ExpandCGHcall	Expands result fron CGHcall to CGHcall object.
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 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-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.summary	Visualization of aCGH profiles.
plot.summary-method	Class to contain and describe called array comparative genomic hybridization data.
postsegnormalize	Post-segmentation normalization
preprocess	Preprocess arrayCGH 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.
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.
segmentData	Breakpoint detection for arrayCGH 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.
Wilting	Cervical cancer arrayCGH data