class.cghRegions: Class to contain and describe array comparative genomic...

In tgac-vumc/CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

Description

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.

Extends

Directly extends class eSet.

Creating Objects

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.

Slots

Inherited from eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to 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:AssayData

phenoData:

See eSet

featureData:

An AnnotatedDataFrame with columns Chromosome, Start, End, Nclone, and Avedist containing region and position information.

experimentData:

See eSet

annotation:

See eSet

Methods

Class-specific methods.

regions(cghRegions), regions(cghRegions,matrix)<-

Access and set elements named regions in the AssayData-class slot.

chromosomes, bpstart, bpend, nclone, avedist

Access the region and position information stored in featureData

plot.cghRegions

Create a plot displaying chromosomes on the Y-axis and base pair position on the X-axis. A new region is displayed by a slight jump with respect to the previous region. Each region is displayed as a bi-colored segment, the lower and upper part of which correspond to the proportions pl and pg of samples with a loss (red) or gain (green), respectively. The color coding is displayed as well: 1: pl (pg) < 10%; 2: 10% = pl (pg) < 30%; 3:30% = pl (pg) < 50%; 4: pl (pg) = 50%.

frequencyPlot

Create a frequency plot

See eSet for derived methods. Annotation functionality is not yet supported.

Author(s)

Sjoerd Vosse

See Also

eSet, cghRaw-class, cghSeg-class, cghCall-class

Examples

	# create an instance of cghRegions
	new("cghRegions")
	
	# load an instance of cghRegions
	data(WiltingRegions)
		
	# plot all region data
	plot(WiltingRegions)
	# make a frequency plot
	frequencyPlot(WiltingRegions)
	
	# extract the region values
	values <- regions(WiltingRegions)
	
	# get the names of the samples
	sampleNames(WiltingRegions)

tgac-vumc/CGHbase documentation built on May 31, 2019, 8:59 a.m.