SGOL-class {cghMCR} | R Documentation

## Class "SGOL" reprents segments of gain or loss across samples

### 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)

[Package cghMCR version 1.48.0 Index]