F Scores of Algorithms Over Three Cell Types from the “Double Hit” Protocol.

Each algorithm was evaluated to gauge the enrichment of short read tags in each of the three cell types obtained from University of Washington “double hit” protocol [27]. The overlap of peaks from each of the cell types was measured against the cell type's “reference set of regulatory regions”. The accuracy of each algorithm was defined as the value of the F score (see Methods for more details) by running it over a range of thresholds. The dashed vertical grey line depicts the value of F score when the algorithm is run with its default parameter. Note that Hotspot failed when ran with  = 0.3 for HelaS3 cell type and therefore its corresponding curve is shorter by one data point.