| cghSeg {CGHbase} | R Documentation |
Container for aCGH data and experimental
metadata. cghSeg class is derived from
eSet, and requires a matrix named copynumber as well as a
matrix named segmented as assayData members of equal dimensions.
Furthermore, columns named Chromosome, Start, and End are
required as featureData members, containing feature position information.
Directly extends class eSet.
new('cghSeg',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
copynumber = [matrix],
segmented = [matrix],
featureData = [AnnotatedDataFrame],
...)
An object of class cghSeg is generally obtained as output
from segmentData.
Inherited from eSet:
assayData:nrow(phenoData). assayData must contain matrices
copynumber and segmented with rows represening array probes
and columns representing samples. Additional matrices of
identical size (e.g., representing measurement errors) may
also be included in assayData. Class:AssayData-classphenoData:eSetfeatureData:AnnotatedDataFrame with columns
Chromosome, Start, and End containing array element position
data.experimentData:eSetannotation:eSetClass-specific methods.
copynumber(cghSeg), copynumber(cghSeg,matrix)<-copynumber in the AssayData-class
slot.segmented(cghSeg), segmented(cghSeg,matrix)<-segmented in the AssayData-class
slot.chromosomes, bpstart, bpendfeatureData
See eSet for derived methods.
Sjoerd Vosse
eSet-class, cghRaw-class, cghCall-class
# create an instance of cghSeg
new("cghSeg")
# load an instance of cghSeg
data(WiltingSeg)
# plot the first sample
# plot.cghSeg(WiltingSeg[,1])
# first three chromosomes
# plot.cghSeg(WiltingSeg[chromosomes(WiltingSeg)==1,1])
# get the copynumber values of the third and fourth sample
log2ratios <- copynumber(WiltingSeg[,3:4])
# get the names of the samples
sampleNames(WiltingSeg)
# get the names of the array elements
featureNames(WiltingSeg)