segments is a data frame extracted from the
"output" element of the object returned by segment of the
package DNAcopy 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 span
alteredLow
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 span
alteredHigh
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 span
recurrence
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/losses with ocurrence rate grater
than the threshold values are declared as MCRs
spanLimit
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 time
thresholdType
thresholdType is a character string that
can be either "quantile" or "value" indicating wether
alteredLow or alteredHigh is quantial or actual value
Value
An object of the cghMCR class
Details
The function is just a constructor of the cghMCR class
for the instantiation of a cghMCR object