## Copy number aberrations / Fuse regions by column value

### Description

Fuses together consecutive regions based on column values, e.g. those with a significant p-value.

### Parameters

- column (...) [pvalue]
- is (smaller than, smaller than or equal to, equal to, larger than or equal to, larger than, not equal to, within, outside) [smaller than]
- cutoff [0.05]

### Details

This tool fuses together consecutive regions that match a user-specified criteria. This can be handy when doing a statistical test between groups or for survival and obtaining a number of consecutive regions with a significant pvalue. This tool allows these consecutive regions to be combined into one, and statistical tests then repeated yielding new p-values for the larger region.

In addition to the table of regions, this tool also needs as an input file the original data file with the original features where the regions where derived from.

### Output

A table with new 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