Copy number aberrations / Survival test for called copy number data

Description

Statistical test for survival and called copy number data. The testing is recommended to be performed after running the Identify common regions from called aCGH data tool.

Parameters

• Phenodata column with survival data
• Phenodata column with survival status (1=dead, 0=alive)
• Number of permutations (...) [10000]
• Aberrations to test (losses, gains, both) [both]

Details

Perform the logrank test for survival with called copy number data. The significance of the p-values is evaluated through permutations, and a false discovery rate is calculated. At least 10,000 permutations are recommended for final calculations, and this will require a significant amount of time. Testing can be performed only for gains/losses, or both.

Output

The input table appended with with p-values and false discovery rates.

References

Wiel et al. (2005) CGHMultiArray: exact p-values for multi-array comparative genomic hybridization data. Bioinformatics 21: 3193-3194