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.
...

This script runs the local score on your data. The user should change the filename 'quailfreqs.txt' to the name of his file. The formating of this file is explained in the script.

These are the scripts used in the article Quantitative trait loci (QTL) with small effects, which are pervasive in quantitative phenotypic variation, are difficult to detect in genome-wide association studies (GWAS). (Bonhomme et al. 2019). [[https://www.nature.com/articles/s41437-019-0235-x]]
...

This document contains all the functions that are used on de localscore.R script. It should be saved on the same directory that localscore.R