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(Wilting)
  ## Convert to this-is-escaped-codenormal-bracket27bracket-normal object
  cgh <- make_cghRaw(Wilting)
  ## First preprocess the data
  raw.data <- preprocess(cgh)
  ## Simple global median normalization for samples with 75% tumor cells
  perc.tumor <- rep(0.75, 3)
  normalized.data <- normalize(raw.data, cellularity=perc.tumor)  
  ## Segmentation with slightly relaxed significance level to accept change-points.
  ## Note that segmentation can take a long time.
  ## Not run: segmented.data <- segmentData(normalized.data, alpha=0.02)

[Package CGHcall version 1.2.0 Index]