CNSeg-class: 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

Arguments

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

References

Examples

Run this code

   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

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