cghMCR {cghMCR}R Documentation

The constructor for the cghMCR class

Description

Instantiates a cghMCR object using the parameters passed.

Usage

cghMCR(segments, margin = 0, gain.threshold = 0.5, loss.threshold = -0.5)

Arguments

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

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

  require("cghMCR")
  data("sampleData")
  segments <- getSegments(sampleData)
  cghmcr <- cghMCR(segments, margin = 0, gain.threshold = 0.8,
                 loss.threshold = -0.8)

[Package cghMCR version 1.2.0 Index]