cghMCR {cghMCR} | R Documentation |
Instantiates a cghMCR object using the parameters passed.
cghMCR(segments, margin = 0, gain.threshold = 0.5, loss.threshold = -0.5)
segments |
segments is a data frame extracted from the
"output" element of the object returned by segment of the
package DNAcopy or getSegments |
margin |
margin is a integer specifying how far apart two
adjacent segments are allowed to be considered to be the same locus |
gain.threshold |
gain.threshold is a positive integer
specifying the reshold log2 ratio when a segment of chromosome
can be considered to be a gain |
loss.threshold |
loss.threshold is a negative integer
specifying the reshold log2 ratio when a segment of chromosome can
be considered to be a loss |
The function is just a constructor of the cghMCR
class
for the instantiation of a cghMCR object
An object of the cghMCR class
The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute
Jianhua Zhang
References on S4 class
require("cghMCR") data("sampleData") segments <- getSegments(sampleData) cghmcr <- cghMCR(segments, margin = 0, gain.threshold = 0.8, loss.threshold = -0.8)