cghCall {CGHbase} | R Documentation |
Container for aCGH data and experimental
metadata. cghCall
class is derived from
eSet
, and requires the following matrices of equal dimension
as assayData members:
copynumber
Log2 copynumber ratios.
segmented
Segmented log2 ratios.
calls
Called copynumer values.
probloss
Loss probabilities as returned by CGHcall
.
probnorm
Normal probabilities as returned by CGHcall
.
probgain
Gain probabilities as returned by CGHcall
.
probamp
Optional amplification probabilities as returned by CGHcall
when run with nclass=4
.
Furthermore, columns named Chromosome
, Start
, and End
are
required as featureData members, containing feature position information.
Directly extends class eSet
.
new('cghCall',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
copynumber = [matrix],
segmented = [matrix],
calls = [matrix],
probloss = [matrix],
probnorm = [matrix],
probgain = [matrix],
featureData = [AnnotatedDataFrame],
...)
An object of class cghCall
is generally obtained as output
from CGHcall
.
Inherited from eSet
:
assayData
:nrow(phenoData)
. assayData
must contain the following matrices
copynumber
Log2 copynumber ratios.
segmented
Segmented log2 ratios.
calls
Called copynumer values.
probloss
Loss probabilities as returned by CGHcall
.
probnorm
Normal probabilities as returned by CGHcall
.
probgain
Gain probabilities as returned by CGHcall
.
probamp
Optional amplification probabilities as returned by CGHcall
when run with nclass=4
.
assayData
. Class:AssayData-class
phenoData
:eSet
featureData
:AnnotatedDataFrame
with columns
Chromosome
, Start
, and End
containing array element position
data.experimentData
:eSet
annotation
:eSet
Class-specific methods.
copynumber(cghCall)
, copynumber(cghCall,matrix)<-
copynumber
in the AssayData-class
slot.segmented(cghCall)
, segmented(cghCall,matrix)<-
segmented
in the AssayData-class
slot.calls(cghCall)
, calls(cghCall,matrix)<-
calls
in the AssayData-class
slot.probloss(cghCall)
, probloss(cghCall,matrix)<-
probloss
in the AssayData-class
slot.probnorm(cghCall)
, probnorm(cghCall,matrix)<-
probnorm
in the AssayData-class
slot.probgain(cghCall)
, probgain(cghCall,matrix)<-
probgain
in the AssayData-class
slot.chromosomes
, bpstart
, bpend
featureData
See eSet
for derived methods.
Sjoerd Vosse
eSet-class
, cghRaw-class
, cghSeg-class
# create an instance of cghCall new("cghCall") # load an instance of cghCall data(WiltingCalled) # plot the first sample plot.cghCall(WiltingCalled[,1]) # plot the first chromosome of the first sample plot.cghCall(WiltingCalled[chromosomes(WiltingCalled)==1,1]) # get the copynumber values of the third and fourth sample log2ratios <- copynumber(WiltingCalled[,3:4]) # get the names of the samples sampleNames(WiltingCalled) # get the names of the array elements featureNames(WiltingCalled)