aCGH / Identify common regions from called aCGH data

Description

Reduces dimensionality of called aCGH data by identifying common breakpoints.

Parameters

Details

Reduce dimensionality of called aCGH data be compressing adjacent probes 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A table where probes have been replaced by chromosomal regions. The number of probes in each region is also returned.

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.

A plot illustrating the frequencies of losses (left scale) and gains (inverted left scale).

References

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