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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(CNTools)
Loading required package: tools
Loading required package: genefilter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CNTools/CNSeg-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CNSeg-class
> ### Title: Class "CNSeg" contains the output of DNACopy segmentation data
> ###   that can be operated on by the associated methods
> ### Aliases: CNSeg-class segList sampleData CNSeg segList<- segList-method
> ###   segList,CNSeg-method segList<-,CNSeg-method show,CNSeg-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"]), 10))), ])
>    rsBypair <- getRS(seg, by = "pair", imput = FALSE, XY = FALSE, what = "mean")

Processing samples .......... done
>    rsBypair
Object of RS
Number of pairs: 45
Segment data converted based on pair
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>