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-class
phenoData
:eSet
featureData
:AnnotatedDataFrame
with columns
Chromosome
, Start
, and End
containing array element position
data.experimentData
:eSet
annotation
:eSet
Class-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
, bpend
featureData
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)