CGHtest: hypothesis testing for arrayCGH regions based on calls.

CGHtest currently includes: Wilcoxon-Mann-Whitney two-sample test (see also
Van de Wiel et al. (2005) CGHMultiArray: Exact p-values for multi-array CGH-data, Bioinformatics, 21, 3193-3194.); Kruskal-Wallis k-sample test; Chi-Square association test ; Binomial proportion test (e.g. proportion 'gain' in one group vs proportion 'gain' in the other group(s)) and multiple comparisons. CGHlogrank includes the logrank test for association of aberrations with survival data. False Discovery Rates (FDR) are estimated based on the entire set of tests performed. 

The input files need to be produced by CGHregions.
The R-package: 
(Windows); CGHtest_1.1.tar.gz (Linux,Unix; not tested)

The R-package, allowing for parellel computing: 
(Windows); CGHtestpar_0.0.tar.gz (Linux,Unix; not tested)

Example script