AllAccessors: '"rCGH"' Accessor Functions

In fredcommo/rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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"))

fredcommo/rCGH documentation built on May 16, 2019, 2:41 p.m.