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 getSegments
gapAllowed
: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)