Can someone please explain in detail the meaning of the following section of the paper 2.2 Finding a candidate QTL per phenotype For simplicity, we will focus on a single molecular phenotype P quantified in a set of N samples. Let G be the set of genotype dosages at L variant sites located within a cis-window of 6 W Mb of the genomic location of P. To discover the best candidate QTL for P, FastQTL measures Pearson product-moment correlation coefficients between P and all L variants in G, stores the most strongly correlated variant q [ G as candidate QTL, and assesses its significance by calculating a nominal P-value pn with standard significance tests for Pearson correlation. How can this be affected by a test where only one SNP and its LD proxies (r=0.8) is tested. Thanks!
Please see: C: FastQTL - GNU Scientific Library (GSL) Domain Error