CNSeg-class {CNTools} | R Documentation |
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 can be created by calls of the form new("CNSeg",..)
.
A constructor CNSeg(segList)
can also be used to instantiate
CNSeg object
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
signature(object = "CNSeg")
: get the
Reduced Segment data matrix
signature(object = "CNSeg")
: get the
value for slot "segList" of a CNSeg object
signature(object = "CNSeg")
: set the
value for slot "segList" of a CNSeg object
signature(object = "CNSeg")
: print a CNSeg
object
Jianhua Zhang
NA
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