RS-class {CNTools} | R Documentation

## Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation

### Description

The class contains the Reduced Segment data matrix derived from the output of the segment method of DNACopy and provides functions to manipulate the data or perform other computational operations

### Objects from the Class

Objects can be created by calls of the form `new("RS", ...)`. A constructor RS(rs, by, imput, XY) can also be used to intantiate an object of this class

### Slots

`rs`:

  Object of class `"ANY"` eith a matrix if the RS is by region or gene or a list of matrix if the RS is by sample pairs

`by`:

  Object of class `"character"` a charactere string indicating how the RS matrix is obtained. Valid values include region, gene, or pair

### Methods

cor

  `signature(x = "RS")`: Calculates the sample wise correlation coefficients using the Reduced Segment matix

dist

  `signature(x = "RS")`: Calculates the distance between samples contained in the Reduced Segment matrix

genefilter

  `signature(expr = "RS")`: filters features by calling the genefilter function

madFilter

  `signature(object = "RS")`: filters features by mean absolute deviation

rs

  `signature(object = "RS")`: get method for the by slot of an RS object

rs<-

  `signature(object = "RS")`: assignment method for the rs slot

segBy

  `signature(object = "RS")`: get method for the by slot of an RS object

show

  `signature(object = "RS")`: show method for an RS object

### Author(s)

Jianhua Zhang

### See Also

`CNSeg`

### Examples

        data("sampleData")
        # take a subset of the data for speed
        seg <- CNSeg(sampleData[which(is.element(sampleData[, "ID"], sample(unique(sampleData[, "ID"]), 20))), ])
        rsByregion <- getRS(seg, by = "region", imput = TRUE, XY = FALSE, what = "median")
        rsByregion

[Package CNTools version 1.42.0 Index]