So, what does a peak-caller do?
The background forms a signal with ridges and valleys. So does the experiment. In Figure 1, the experiment signal is shown in red, the background signal is shown in blue, and peaks are shown as green boxes. If we compare the experiment signal to the background signal, we get three basic results:
- the experiment signal is lower than the background signal (second)
- the experiment signal is equal to the background signal (not shown)
- the experiment signal is larger than the background signal (first, third, and fourth).
While case (1) might happen due to the variation in the measurements. Anyway in both cases (1) and (2), we can safely assume that there is no modification of the histone due to our measurements. Case (3), however, is not that obvious. In fact, here, we need to check how much larger the experiment signal is compared to the background signal. For this, a statistical analysis is used. If the experiment is significantly larger than the background, a modified histone is assumed (first, third) otherwise an un-modified histone is assumed (fourth). This allows to find segments of the genome that are unmodified and those that are modified. The modified segments are called peaks and are reported by the peak-callers.