SGOL-class: Class "SGOL" reprents segments of gain or loss across samples
Description
Segments of gains or losses along chromosomes can be
calculated based on segmentation data derived from the segment
function of the DNAcopy package
Arguments
Objects from the Class
Objects can be created by calls of the form new("SGOL", ...) or
using a constructor SGOL.
Slots
gol:
Object of class "matrix" holding the gain
or loss data for chromosomal segments
threshold:
Object of class "vector" of length 2
indicating the lower and upper thresholds below/over which data
points will be included in the calculation of SGOL score using the
method defined by method
method:
Object of class "function" giving the
method used to calculate SGOL scores. Common methods include sum,
median, and mean
Methods
gol
signature(object = "SGOL"): extracts SGOL scores
method
signature(object = "SGOL"): gets the name of
the function used to calculate the SGOL scores
plot
signature(x = "SGOL", y = "ANY",...): plots the data
threshold
signature(object = "SGOL"): gets the
thredhold used for the calculation
References
The SGOL score is a modified version of the GISTIC score
published in PNAS 104: 20007-20012