rCGH (version 1.2.2)

AllAccessors: "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

## S3 method for class 'rCGH':
getInfo(object, item = NULL)
## S3 method for class 'rCGH':
getCNset(object)
## S3 method for class 'rCGH':
getParam(object)
## S3 method for class '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.

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"))