cghCall {CGHcall} | 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
segmented
calls
probloss
probnorm
probgain
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
segmented
calls
probloss
probnorm
probgain
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") # create an instance of cghCall through this-is-escaped-codenormal-bracket153bracket-normal ## Not run: data(Wilting) rawcgh <- make_cghRaw(Wilting) cghdata <- preprocess(cghdata) normalized <- normalize(cghdata) segmented <- segmentData(normalized) called <- CGHcall(segmented) # plot the first sample plot(called[,1]) # plot the first chromosome of the first sample plot(called[chromosomes(called)==1,1]) # get the copynumber values of the third and fourth sample log2ratios <- copynumber(called[,3:4]) # get the names of the samples sampleNames(called) # get the names of the array elements featureNames(called) ## End(Not run)