Description Objects from the Class Slots Methods Author(s) References Examples

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

Objects can be created by calls of the form `new("SGOL", ...)`

or
using a constructor SGOL.

`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

- 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

Jianhua Zhang

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

1 2 |

```
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
```

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