Description Usage Arguments Details Value Warning Author(s) References See Also Examples
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.
1 | regioning(cghdata.called, threshold = 1e-05)
|
cghdata.called |
Object of class |
threshold |
Threshold for the function |
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).
A list
-object with the following entries:
ann |
|
hardcalls |
The regioned hard calls |
softcalls |
The regioned soft calls |
The current version of CGHregions is designed for hard calls only. This is likely to change in the near future, making this function obsolete.
Wessel N. van Wieringen: w.vanwieringen@vumc.nl
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
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