AllAccessors {rCGH} | R Documentation

## `"rCGH"` Accessor Functions

### Description

Methods for extracting information from an object of class `"rCGH"`.
Each of the below methods are simply convenience functions which extract the corresponding slots (as the name of each method suggests) from an object of class `"rCGH"`.

### Usage

    ## S4 method for signature 'rCGH'
    getInfo(object, item = NULL)
    ## S4 method for signature 'rCGH'
    getCNset(object)
    ## S4 method for signature 'rCGH'
    getParam(object)
    ## S4 method for signature 'rCGH'
    getSegTable(object, minLen = NULL)

### Arguments

`object` | : An object of class `"rCGH"`
`item` | : character. Can be one, or a vector of items. When `NULL`, the full available information is returned. If `item` is specified, and exists, the corresponding value(s) only is(are) returned.
`minLen` | : numeric. The mininal length for a segment, in Kb. When `NULL` (default), the segmentation table is exported, as it has been computed with `segmentCGH`, segments shorter than the specified value are re-merged otherwise.

### Value

- getInfo(object, item = NULL): character.

- getCNset(object): a data frame.

- getParam(object): a list of parameters.

- getSegTable(object, minLen = NULL): a data frame.

### Methods

`"rCGH"`

  - getInfo(object, item = NULL): returns the values of the specified items, all the information otherwise.

  - getCNset(object): returns the full by-probe dataset.

  - getParam(object): returns the analysis parameters.

  - getSegTable(object, minLen = NULL): returns the segmentation table - one row per segment.

### Author(s)

Frederic Commo

### See Also

`setInfo`, `segmentCGH`

### Examples

    filePath <- system.file("extdata", "Agilent4x180K.txt.bz2", package = "rCGH")
    cgh <- readAgilent(filePath, sampleName = "Agilent4x180K", labName = "myLab")

    # Getting all the information
    getInfo(cgh)

    # Getting specific items
    getInfo(cgh, c("sampleName", "labName"))

[Package rCGH version 1.20.0 Index]