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 |