segmentData {CGHcall}R Documentation

Breakpoint detection for arrayCGH data.

Description

A wrapper function to run existing breakpoint detection algorithms on arrayCGH data. Currently only DNAcopy is implemented.

Usage

segmentData(input, method = "DNAcopy", ...)

Arguments

input Object of class cghRaw.
method The method to be used for breakpoint detection. Currently only 'DNAcopy' is supported, which will run the segment function.
... Arguments for segment.

Details

See segment for details on the algorithm.

Value

This function returns a dataframe in the same format as the input with segmented arrayCGH data.

Author(s)

Sjoerd Vosse & Mark van de Wiel

References

Venkatraman, A.S., Olshen, A.B. (2007). A faster circulary binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663.

Examples

  data(WiltingNorm)
  ## Not run: segmented.data <- segmentData(WiltingNorm, alpha=0.02)

[Package CGHcall version 2.0.0 Index]