Figure 3
Enrichment and peak detection processes.
Two replicate datasets (coloured lines) and their average (black line) are represented along with the probe positions (coloured boxes). The cut-off value calculated for the particular dataset is shown (dashed line). All probes with all values above this cut-off are identified in the first stage of the enrichment detection procedure (highlighted probes). Windows around these probes are analysed (demonstrated with grey boxes for one probe in box (a)) to determine which, if any, windows contain probes deemed to be enriched over the whole window region. The first window extends upstream from the probe being analysed (as indicated by the arrow). The next window extends upwards from the furthest probe in this window, but not including it (as indicated by the arrow) and this process is repeated for all probes until the initial identified probe is reached. In this way all possible windows are identified for analysis. If the initial probe is found to be in any enriched window it is returned as an enriched probe by the software, whereas if it is not found to be in any enriched window it is not. If peak detection is required, averaged data are used to identify all maxima within the enriched probes (black crosses), each of which is returned as one peak. Maxima within individual datasets are also identified (coloured crosses) which are used to calculate potential binding regions of each peak (PBRs; demonstrated for one peak in box (b)). The PBR represents the region most likely to contain the binding site of the factor of interest and is defined as half the distance from the maxima to the next probe, up- and downstream of the maxima, unless this is distance is greater than the average chromatin shear size, in which case the distance is set to the average chromatin shear size. Peaks where all maxima fall at the same probe (as ‘i’) will therefore have narrower PBRs than those where they fall at adjacent probes (as ‘iii’). If all probe values are not above the cut-off (as ‘ii’ and ‘iv’) they are not identified as being enriched.
