| cghMCR-class {cghMCR} | R Documentation |
Objects of this class provides the functionalities to detecting chromosome regions that show gains or losses across differnet samples
Objects can be created by calls of the form new("cghMCR", ...).
A constructor cghMCR may be used to instantiate object
of this class
DNASeg:"data.frame" containing
segmentation data derived from segmentation analysis using segment
or getSegmentsgapAllowed:gapAllowed is an
integer specifying low threshold of base pair number to separate two
adjacent segments, belower which the two segments will be joined as
an altered spanalteredLow:alteredLow is a
positive number between 0 and 1 specifying the lower reshold
percential value. Only segments with values falling below this
threshold are considered as altered spanalteredHigh:alteredHigh is a
positive number between 0 and 1 specifying the upper reshold
percential value. Only segments with values falling over this
threshold are considered as altered spanrecurrence:recurrence is an
integer between 1 and 100 that specifies the rate of occurrence for
a gain or loss that are observed across sample. Only gains or losses
with ocurrence rate grater than the threshold values are declared as MCRsspanLimit:spanLimit is an
integer that defines the leangh of altered spans that can be
considered as locus. It is not of any use at this timesignature(object = "cghMCR"): identifies minimum
common regions of gains/losses across samplesThe function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute
Jianhua Zhang
require("cghMCR")
data("sampleData")
segments <- getSegments(sampleData)
cghmcr <- cghMCR(segments, gapAllowed = 500, alteredLow = 0.20,
alteredHigh = 0.80, recurrence = 50)