Local score

This section contains R scripts allowing computing the local score, and the associated significance regions, from the p-values of a single-marker test. For the computation of significance thresholds, it is assumed that the local score has a Gumble distribution under the null hypothesis, which holds asymptotically for long score sequences. The parameters of the Gumbel are obtained by Monte Carlo simulations, which account for the observed correlation between scores.

The input p-value file corresponds here to the FLK analysis of two quail lines described in Fariello et al (2017), for chromosomes 4 to 28 (which can be downloaded from the Files tab), but this file can be replaced by any other file with appropriate format.