SGOL-class: Class "SGOL" reprents segments of gain or loss across samples

In cghMCR: Find chromosome regions showing common gains/losses

Description

Segments of gains or losses along chromosomes can be calculated based on segmentation data derived from the segment function of the DNAcopy package

Objects from the Class

Objects can be created by calls of the form new("SGOL", ...) or using a constructor SGOL.

Slots

gol:

Object of class "matrix" holding the gain or loss data for chromosomal segments

threshold:

Object of class "vector" of length 2 indicating the lower and upper thresholds below/over which data points will be included in the calculation of SGOL score using the method defined by method

method:

Object of class "function" giving the method used to calculate SGOL scores. Common methods include sum, median, and mean

Methods

gol

signature(object = "SGOL"): extracts SGOL scores

method

signature(object = "SGOL"): gets the name of the function used to calculate the SGOL scores

plot

signature(x = "SGOL", y = "ANY",...): plots the data

threshold

signature(object = "SGOL"): gets the thredhold used for the calculation

Author(s)

Jianhua Zhang

References

The SGOL score is a modified version of the GISTIC score published in PNAS 104: 20007-20012

Examples

showClass("SGOL")
require(CNTools)

Example output

Loading required package: DNAcopy
Loading required package: CNTools
Loading required package: tools
Loading required package: genefilter
Loading required package: limma
Class "SGOL" [package "cghMCR"]

Slots:
                                       
Name:         gol  threshold     method
Class: data.frame     vector   function

cghMCR documentation built on Nov. 8, 2020, 7:46 p.m.