cghCall {CGHbase} | R Documentation

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

### Description

Container for aCGH data and experimental metadata. `cghCall` class is derived from `eSet`, and requires the following matrices of equal dimension as assayData members:

- `copynumber` Log2 copynumber ratios.
- `segmented` Segmented log2 ratios.
- `calls` Called copynumer values.
- `probloss` Loss probabilities as returned by `CGHcall`.
- `probnorm` Normal probabilities as returned by `CGHcall`.
- `probgain` Gain probabilities as returned by `CGHcall`.
- `probamp` Optional amplification probabilities as returned by `CGHcall` when run with `nclass=4`.

Furthermore, columns named `Chromosome`, `Start`, and `End` are required as featureData members, containing feature position information.

### Extends

Directly extends class `eSet`.

### Creating Objects

`new('cghCall', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], calls = [matrix], probloss = [matrix], probnorm = [matrix], probgain = [matrix], featureData = [AnnotatedDataFrame], ...)`

An object of class `cghCall` is generally obtained as output from `CGHcall`.

### Slots

Inherited from `eSet`:

`assayData`:
  Contains matrices with equal dimensions, and with column number equal to `nrow(phenoData)`. `assayData` must contain the following matrices
  - `copynumber` Log2 copynumber ratios.
  - `segmented` Segmented log2 ratios.
  - `calls` Called copynumer values.
  - `probloss` Loss probabilities as returned by `CGHcall`.
  - `probnorm` Normal probabilities as returned by `CGHcall`.
  - `probgain` Gain probabilities as returned by `CGHcall`.
  - `probamp` Optional amplification probabilities as returned by `CGHcall` when run with `nclass=4`.
  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(cghCall)`, `copynumber(cghCall,matrix)<-`
  Access and set elements named `copynumber` in the `AssayData-class` slot.
`segmented(cghCall)`, `segmented(cghCall,matrix)<-`
  Access and set elements named `segmented` in the `AssayData-class` slot.
`calls(cghCall)`, `calls(cghCall,matrix)<-`
  Access and set elements named `calls` in the `AssayData-class` slot.
`probloss(cghCall)`, `probloss(cghCall,matrix)<-`
  Access and set elements named `probloss` in the `AssayData-class` slot.
`probnorm(cghCall)`, `probnorm(cghCall,matrix)<-`
  Access and set elements named `probnorm` in the `AssayData-class` slot.
`probgain(cghCall)`, `probgain(cghCall,matrix)<-`
  Access and set elements named `probgain` in the `AssayData-class` slot.
`chromosomes`, `bpstart`, `bpend`
  Access the chromosomal positions stored in `featureData`
plot.cghCall
  Create a plot containing log2ratios, segments and call probabilities ordered by chromosomal position
summaryPlot
  Create a plot summarizing the call probabilities of all samples

See `eSet` for derived methods.

### Author(s)

Sjoerd Vosse

### See Also

`eSet-class`, `cghRaw-class`, `cghSeg-class`

### Examples

            # create an instance of cghCall
            new("cghCall")

            # load an instance of cghCall
            data(WiltingCalled)

      # plot the first sample
      plot.cghCall(WiltingCalled[,1])

      # plot the first chromosome of the first sample
      plot.cghCall(WiltingCalled[chromosomes(WiltingCalled)==1,1])

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

      # get the names of the samples
      sampleNames(WiltingCalled)

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

[Package CGHbase version 1.2.0 Index]