Footprint symmetry score #88
Description
Hello!
I wonder if you can provide codes to calculate the footprint symmetry score as described in the version 1 paper (Genome Biology), for example, from output of run_centipede_parker.R: *lambda.txt
CUT&RUNTools has built in a feature to determine whether a motif footprint is primary or secondary, based on a “footprint symmetry score” (FSS) defined as follows. The footprint profile is first divided in the middle into two halves, and to capture shape information, each half is fitted by an exponential decay curve (of the form Aleft exp (B left × x) and A right exp (Bright ) × x, respectively) (Fig. 3). The parameter B left (and Bright ) reflects the ascent rate for the left arm (and the “descent rate” for the right arm). The goodness of fit is quantified using the R2 statistic, represented by R left 2 and Rright 2 . The FSS score is defined as B left × R left 2 + − 1 × B right × Rright 2 . Intuitively, the FSS score measures the rate of increase of cut probabilities in the footprint plot, as the position approaches the motif. This rate should match the respective rate of decrease of cut probabilities as the position is further away from center. A FSS score of > 0.3 and a small difference between B left and − 1 × B right indicate symmetry of motif footprint. Such a motif is designated primary.