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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(CNTools)
Loading required package: tools
Loading required package: genefilter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CNTools/RS-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RS-class
> ### Title: Class "RS" contains the Reduced Segment data matrix derived from
> ###   the output of segmentation
> ### Aliases: RS-class rs<- rs segBy rs,RS-method rs<-,RS-method
> ###   segBy,RS-method show,RS-method
> ### Keywords: classes
> 
> ### ** 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")
Processing samples ... Done
>     rsByregion
Object of RS
	Number of regions = 4808
	Number of samples = 20

Segment data converted based on region
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>