Calling aberrations for array CGH tumor profiles.


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Documentation for package ‘CGHcall’ version 2.12.0

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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