CGHcall {CGHcall}R Documentation

Calling aberrations for array CGH tumor profiles.

Description

Calls aberrations for array CGH data using a six state mixture model.

Usage

CGHcall(inputSegmented, prior = "auto", nclass = 3, organism = "human")

Arguments

inputSegmented An object of class cghSeg
prior Options are all, not all, or auto. See details for more information.
nclass The number of levels to be used for calling. Either 3 (loss, normal, gain) or 4 (including amplifications).
organism Either human or other. This is only used for chromosome arm information when prior is set to all or auto (and samplesize > 20).

Details

Please read the article and the supplementary information for detailed information on the algorithm.

The parameter prior states how the data is used to determine the prior probabilities. When set to all, the probabilities are determined using the entire genome of each sample. When set to not all probabilites are determined per chromosome for each sample when organism is set to other or per chromosome arm when organism is human. The chromosome arm information is taken from the March 2006 version of the UCSC database. When prior is set to auto, the way probabilities are determined depends on the sample size. The entire genome is used when the sample size is smaller than 20, otherwise chromosome (arm) information is used.

Please note that CGHcall uses information from all input data to determine the aberration probabilities. When for example triploid or tetraploid tumors are observed, we advise to run CGHcall separately on those (groups of) samples.

Value

This function return a list with three components:

probabilities A dataframe with 3 columns of probe information (name, chromosome and position), followed by k columns with aberration probabilities for each sample, where k is the number of levels used for calling (nclass).
calls A dataframe with the calls for each sample. Values are -1 (loss), 0 (normal) or 1 (gain). If 4 levels were used for calling, a value of 2 represents an amplification.
segments A matrix with the segments for each profile. The first column contains the sample number. The second column the level of the current segment and the third and fourth columns the start and end of the segment in probe number respectively.

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.

Examples


  data(WiltingSeg)
  ## Not run: result <- CGHcall(WiltingSeg)


[Package CGHcall version 2.0.0 Index]