## Copy number aberrations / Identify common regions from called copy number data

### Description

Reduces dimensionality of called copy number data by identifying common breakpoints.

### Parameters

- Maximum amount of information loss allowed (0...1) [0.01]

### Details

Reduce dimensionality of called aCGH data be compressing adjacent data points into single data points when their signature is shared between all of the samples. Some loss of information is allowed, and this threshold can be set by the user.

### Output

A table where original data points (probes or bins) have been replaced by chromosomal regions. The number of data points in each region is also returned.

A PDF containing two plots: 1) frequencies of losses (red) and gains (blue), and 2) a plot showing each chromosome as a horizontal line, with each breakpoint bumping the vertical position of the line. On top of this black line, frequencies of losses/gains are shown in red/green.

### References

Wiel et al. (2007) CGHregions: Dimension reduction for array CGH data with minimal information loss. Cancer Informatics 3: 55-63