CNSeg-class {CNTools} | R Documentation

## Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods

### Description

Segmentation results of copy number data can not be operated by other analysis tools such as classification. The class "CNSeg" provides methods to convert segmentation data into a (what is called Reduced segments (RS))matrix format so that other computations can be performed

### Objects from the Class

Objects can be created by calls of the form `new("CNSeg",..)`. A constructor `CNSeg(segList)` can also be used to instantiate CNSeg object

### Slots

`segList`:

  Object of class `"data.frame"` is the "output" element of the object return by the segment function of DNACopy

`chromosome`:

  Object of class `"character"` is the name of the column in segList that contains the chromosome name a given segment belong to

`end`:

  Object of class `"character"` is the name of the column in segList that contains the ending locatino of a given segment

`start`:

  Object of class `"character"` is the name of the column in segList that contains the starting location of a given segment

`segMean`:

  Object of class `"character"` is the name of the column in segList that contains the mean log ratio of a given segment

`id`:

  Object of class `"character"` is the name of the column in segList that contains the id of a given segment

### Methods

getRS

  `signature(object = "CNSeg")`: get the Reduced Segment data matrix

segList

  `signature(object = "CNSeg")`: get the value for slot "segList" of a CNSeg object

segList<-

  `signature(object = "CNSeg")`: set the value for slot "segList" of a CNSeg object

show

  `signature(object = "CNSeg")`: print a CNSeg object

### Author(s)

Jianhua Zhang

### References

NA

### See Also

`RS`

### Examples

       data("sampleData")
       # take a subset of the data for speed
       seg <- CNSeg(sampleData[which(is.element(sampleData[, "ID"],
           sample(unique(sampleData[, "ID"]), 10))), ])
       rsBypair <- getRS(seg, by = "pair", imput = FALSE, XY = FALSE, what = "mean")
       rsBypair

[Package CNTools version 1.42.0 Index]