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

  Create a plot containing log2ratios and segments ordered by chromosomal position. TWO EXTRA OPTIONS PLUS DEFAULTS: dotres=10. Every dotres-th log2-ratio is plotted. dotres=1 plots all data. However, higher values save a lot of space and allow quicker browsing of the plots. ylimit=c(-2,5): limits of the y-axis

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")

    # create an instance of cghSeg through \code{segmentData}
    ## Not run:
       data(Wilting)
       rawcgh <- make_cghSeg(Wilting)
       normalized <- normalize(rawcgh)
       segmented <- segmentData(normalized)

       # plot the first sample. Default only every 10th log2-ratio is plotted (dotres=10). Adjust using dotres= option below.
       plot(segmented[,1])
       # first three chromosomes
       plot(segmented[chromosomes(segmented)<=3,1])

       # get the copynumber values of the third and fourth sample
       log2ratios <- copynumber(segmented[,3:4])

       # get the names of the samples
       sampleNames(segmented)

       # get the names of the array elements
       featureNames(segmented)

    ## End(Not run)

[Package CGHbase version 1.40.0 Index]