CNSeg-class: Class "CNSeg" contains the output of DNACopy segmentation...

In CNTools: Convert segment data into a region by sample matrix to allow for other high level computational analyses.

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

Example output

Loading required package: tools
Loading required package: genefilter

Processing samples .......... done
Object of RS
Number of pairs: 45
Segment data converted based on pair

CNTools documentation built on Nov. 8, 2020, 8:21 p.m.