## Copy number aberrations / Test for copy-number-induced expression changes

### Description

Nonparametric testing for changes in expression induced by a change in DNA copy number. The copy number and expression sets must be matched together beforehand using the Match copy number and expression features tool. The copy number data set can be either a microarray (aCGH) or an NGS (CNA-seq) one. For the expression data, only microarrays have been tested, but in the future RNA-seq or miRNA-seq might also be applicable.

### Parameters

- Test statistic to use (wcvm, wmw) [wcvm]
- Type of analysis (univariate, regional) [univariate]
- Number of permutations (...) [10000]

### Details

Performs a permutation-based non-parametric test to detect genes whose expression has been changed through a change in DNA copy number. Please see the referenced article for details on the two possible test statistics (weighted Cramer-Von Mises or weighted Mann-Whitney), and whether the test statistic should be "shrunken" within a region (regional), or not (univariate).

### Output

A table of matched copy number and expression data, along with p-values of the permutation test. This file can be used to plot expression profiles of individual genes ("Plot copy-number-induced gene expression" tool).

### References

Wieringen et al. (2009) Nonparametric testing for DNA copy number induced differential mRNA gene expression. Biometrics 65: 19-29