regioning: Regioning of called array CGH data

In tgac-vumc/WECCA: Weighted clustering of array CGH data

Description

Region construction in DNA copy number data using hard calls. Given the resulting regions, the mediod call probability (soft calls) signature of each region is calculated.

Usage

  regioning(cghdata.called, threshold = 1e-05)

Arguments

cghdata.called	Object of class cghCall, containing annotion, calls and their probabilities.
threshold	Threshold for the function CGHregions. It determines when a region is enforced.

Details

CGHregions is applied to the calls of an object of class cghCall (as returned by CGHcall version 1.2.0 or higher). Using the regions demarcations the mediod call probability signatures are calculated. The matrix of these mediod signatures are considered the regioned soft call data (see warning below).

Value

A list-object with the following entries:

ann	data.frame containing the annotation data of the regions. The first column contains the region's chromosome information, the second and third its start and end base pair, and the fourth column the number of features constituting the region.
hardcalls	The regioned hard calls matrix.
softcalls	The regioned soft calls matrix.

Warning

The current version of CGHregions is designed for hard calls only. This is likely to change in the near future, making this function obsolete.

Author(s)

Wessel N. van Wieringen: [e-mail]

References

Van de Wiel, M.A., Kim, K.I., Vosse, S.J., Van Wieringen, W.N., Wilting, S.M. , Ylstra, B. (2007), "CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles", Bioinformatics, 23, 892-894.

Van de Wiel, M.A., Van Wieringen, W.N. (2007), "CGHregions: dimension reduction for array CGH data with minimal information loss", Cancer Informatics, 2, 55-63.

Van Wieringen, W.N., Van de Wiel, M.A., Ylstra, B. (2007), "Normalized, segmented or called aCGH data?", Cancer Informatics, 3, 331-337

See Also

CGHregions, CGHcall

Examples

# generate object of cghCall class object
data(WiltingCalled)

# make region data (soft and hard calls)
WiltingRegioned <- regioning(WiltingCalled)

tgac-vumc/WECCA documentation built on May 31, 2019, 9 a.m.