cghRaw {CGHbase} | R Documentation

## Class to contain and describe raw or normalized array comparative genomic hybridization data.

### Description

Container for aCGH data and experimental metadata. `cghRaw` class is derived from `eSet`, and requires a matrix named `copynumber` as assayData member. Furthermore, columns named `Chromosome`, `Start`, and `End` are required as featureData members, containing feature position information.

### Extends

Directly extends class `eSet`.

### Creating Objects

`new('cghRaw', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], featureData = [AnnotatedDataFrame], ...)`

`make_cghRaw` is a function to convert a dataframe or textfile to an object of class `cghRaw`. The input should be either a dataframe or a tabseparated textfile (textfiles must contain a header). The first three columns should contain the name, chromosome and position in bp for each array target respectively. The chromosome and position column must contain numbers only. Following these is a column with log2 ratios for each of your samples. If the input type is a textfile, missing values should be represented as 'NA' or an empty field.

### Slots

Inherited from `eSet`:

`assayData`:

  Contains matrices with equal dimensions, and with column number equal to `nrow(phenoData)`. `assayData` must contain a matrix `copynumber` 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(cghRaw)`, `copynumber(cghRaw,matrix)<-`

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

`chromosomes`, `bpstart`, `bpend`

  Access the chromosomal positions stored in `featureData`

plot

  Create a plot containing log2ratios ordered by chromosomal position

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

### Author(s)

Sjoerd Vosse

### See Also

`eSet-class`, `cghSeg-class`, `cghCall-class`

### Examples

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

    # create an instance of cghRaw from a dataframe
    data(Wilting)
    rawcgh <- make_cghRaw(Wilting)

    # plot the first sample
    plot(rawcgh[,1])
    # first three chromosomes
    plot(rawcgh[chromosomes(rawcgh)==1,1])

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

    # get the names of the samples
    sampleNames(rawcgh)

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

[Package CGHbase version 1.40.0 Index]