cghRegions {CGHbase} | R Documentation

## Class to contain and describe array comparative genomic hybridization regions data.

### 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)

[Package CGHbase version 1.40.0 Index]