| 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-classphenoData:eSetfeatureData:AnnotatedDataFrame with columns
Chromosome, Start, and End containing array element position
data.experimentData:eSetannotation:eSetClass-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, bpendfeatureData
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)