Calling aberrations for array CGH tumor profiles.


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Documentation for package ‘CGHcall’ version 2.10.0

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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
bpend-method Class to contain and describe raw or normalized array comparative
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 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
CGHcall Calling aberrations for array CGH tumor profiles.
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
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 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: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
ExpandCGHcall Expands result fron CGHcall to CGHcall object.
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 segmented array comparative genomic
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
plot-method Class to contain and describe raw or normalized array comparative
plot-method Class to contain and describe segmented array comparative genomic
plot.summary Visualization of aCGH profiles.
plot.summary-method Class to contain and describe called array comparative genomic
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
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
segmentData Breakpoint detection for arrayCGH data.
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
Wilting Cervical cancer arrayCGH data