cghMCR: The constructor for the cghMCR class

In cghMCR: Find chromosome regions showing common gains/losses

Description

Instantiates a cghMCR object using the parameters passed.

Usage

cghMCR(segments, gapAllowed = 500, alteredLow = 0.03, alteredHigh =
0.97, spanLimit = 2e+07, recurrence = 75, thresholdType = c("quantile",
"value")) 

Arguments

segments	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

Details

The function is just a constructor of the cghMCR class for the instantiation of a cghMCR object

Value

An object of the cghMCR class

Note

The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute

Author(s)

Jianhua Zhang

References

References on S4 class

See Also

cghMCR

Examples

  data("segData")
  cghmcr <- cghMCR(segData, gapAllowed = 500,
         alteredLow = 0.20, alteredHigh = 0.80, recurrence = 50)

cghMCR documentation built on Nov. 8, 2020, 7:46 p.m.