Class "cghMCR" is a S4 class for the identification of minimum common regions of gains or losses across samples

Description

Objects of this class provides the functionalities to detecting chromosome regions that show gains or losses across differnet samples

Objects from the Class

Objects can be created by calls of the form new("cghMCR", ...). A constructor cghMCR may be used to instantiate object of this class

Slots

DNASeg:

Object of class "data.frame" containing segmentation data derived from segmentation analysis using segment or getSegments

margin:

Object of class "numeric" indicating how far apart two adjacent segments are allowed to be considered to be of the same locus

gain.threshold:

Object of class "numeric" specificing the value of log2 ratio for chromosome gains

loss.threshold:

Object of class "numeric" specificing the value of negative log2 ratio for chromosome losses

Methods

MCR

signature(object = "cghMCR"): identifies minimum common regions of gains/losses across samples

Note

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

Author(s)

Jianhua Zhang

References

See Also

cghMCR

Examples

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