Consensus peaks

A consensus peak is created on a position of genome where is covered by at least one peak from the output sets of the processed replicates. Accordingly, a consensus peak has the following characteristics:

• Coordinate (i.e., chromosome, start, and stop)
  The coordinate of a consensus peak is the union of the coordinates of the peaks from output sets which overlap that position on the genome. For instance:

  // From the Output set of Replicate 1 chr1 10 20 macs_peak_1 20.9

  // From the Output set of Replicate 2 chr1 15 25 macs_peak_1 14.6

  // The resulting consensus peak chr1 10 25 mspc_peak_1 163.484 Note that the p-values are in -log10 format.

• Value
  The value of each consensus peak is X^2 which is calculated by combining the p-values of the overlapping peaks using Fisher's combined probability test:

  X_i^2 = -2 \times \sum_{i=1}^k \ln(p_i)

where X_i^2 is the value of consensus peak i, and p_i is the p-value of overlapping peaks. For instance, the X^2 of aforementioned consensus peaks is 163.484, which is calculated by combining the p-values of overlapping peaks (i.e., 20.9 and 14.6) using the Fisher's method.