cghSeg {CGHbase} | R Documentation

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

### Description

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.

### Extends

Directly extends class `eSet`.

### Creating Objects

`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`.

### Slots

Inherited from `eSet`:

`assayData`:
  Contains matrices with equal dimensions, and with column number equal to `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`:
  See `eSet`
`featureData`:
  An `AnnotatedDataFrame` with columns `Chromosome`, `Start`, and `End` containing array element position data.
`experimentData`:
  See `eSet`
`annotation`:
  See `eSet`

### Methods

Class-specific methods.

`copynumber(cghSeg)`, `copynumber(cghSeg,matrix)<-`
  Access and set elements named `copynumber` in the `AssayData-class` slot.
`segmented(cghSeg)`, `segmented(cghSeg,matrix)<-`
  Access and set elements named `segmented` in the `AssayData-class` slot.
`chromosomes`, `bpstart`, `bpend`
  Access the chromosomal positions stored in `featureData`
plot.cghSeg
  Create a plot containing log2ratios and segments ordered by chromosomal position

See `eSet` for derived methods.

### Author(s)

Sjoerd Vosse

### See Also

`eSet-class`, `cghRaw-class`, `cghCall-class`

### Examples

            # 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)

[Package CGHbase version 1.2.0 Index]