ExpandCGHcall: Expands result fron CGHcall to CGHcall object.

In CGHcall: Calling aberrations for array CGH tumor profiles.

Description

Expands result from CGHcall function to CGHcall object.

Usage

ExpandCGHcall(listcall,inputSegmented, digits=3, divide=4, memeff = FALSE, fileoutpre="Callobj_",CellularityCorrectSeg=TRUE)

Arguments

listcall	List object; output of function CGHcall
inputSegmented	An object of class cghSeg
digits	Number of decimal digits to be saved in the resulting call object. Allows for saving storage space
divide	Number of batches to divide the work load in. Larger values saves memory, but requires more computing time
memeff	When set to TRUE, memory efficient mode is used: results are written in batches to multiple external files. If FALSE, one output object is provided.
fileoutpre	Only relevant when memeff=TRUE. Define prefix for output file names
CellularityCorrectSeg	If TRUE, corrects segmented and normalized values for cellularity as well

Details

This function is new in version 2.7.0. It allows more memory efficient handling of large data objects. If R crashes because of memory problem, we advise to set memeff = TRUE and increase the value of divide. When multiple files are output (in case of memeff=TRUE) the function combine may be used to combine CGHcall objects.

Value

An object of class cghCall-class either as one object (when memeff = FALSE) or as multiple objects stored in .Rdata files in the working directory (when memeff = FALSE)

Author(s)

Sjoerd Vosse & Mark van de Wiel

References

Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van Wieringen, Saskia M. Wilting and Bauke Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23, 892-894.

See Also

CGHcall, cghCall-class

Examples

  data(Wilting)
  ## Convert to \code{\link{cghRaw}} object
  cgh <- make_cghRaw(Wilting)
  print(cgh)
  ## 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)
  ## 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)
  ## Not run: postsegnormalized.data <- postsegnormalize(segmented.data)
  ## Call aberrations
  ## Not run: result <- CGHcall(postsegnormalized.data, cellularity=perc.tumor)
  ## Not run: result <- ExpandCGHcall(result,postsegnormalized.data)

CGHcall documentation built on Nov. 8, 2020, 11:12 p.m.