| cghRegions {CGHbase} | R Documentation |
Container for aCGH regions data and experimental
metadata. cghRegions class is derived from
eSet, and requires a matrix named regions as
assayData member. Furthermore, columns named Chromosome, Start, End,
Nclone, and Avedist are required as featureData members, containing region
and position information.
Directly extends class eSet.
new('cghRegions',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
regions = [matrix],
featureData = [AnnotatedDataFrame],
...)
An object of this class is generally obtained by running the function CGHregions.
Inherited from eSet:
assayData:nrow(phenoData). assayData must contain a matrix
regions with rows represening regions
and columns representing samples. Additional matrices of
identical size (e.g., representing measurement errors) may
also be included in assayData. Class:AssayDataphenoData:eSetfeatureData:AnnotatedDataFrame with columns
Chromosome, Start, End, Nclone, and Avedist containing region
and position information.experimentData:eSetannotation:eSetClass-specific methods.
regions(cghRegions), regions(cghRegions,matrix)<-regions in the AssayData-class
slot.chromosomes, bpstart, bpend, nclone, avedistfeatureData
See eSet for derived methods. Annotation functionality is not yet supported.
Sjoerd Vosse
# create an instance of cghRegions
new("cghRegions")
# load an instance of cghRegions
data(WiltingRegions)
# plot all region data
plot.cghRegions(WiltingRegions)
# make a frequency plot
frequencyPlot(WiltingRegions)
# extract the region values
values <- regions(WiltingRegions)
# get the names of the samples
sampleNames(WiltingRegions)