We conducted all statistical analyses in R (v ≥ 3.31). We have made the R scripts used in these analyses available on bitbucket at https://bitbucket.org/willseylab/tourette_phase1. Where appropriate, we present data as mean ± the 95% confidence interval (CI). We estimate mean and 95% CI with the t.test function. We describe the value of n in the main text and/or in Tables 1, 2, and 3, and n stands for number of samples (trios), number of base pairs, or number of variants as indicated. We conducted the primary burden analyses with a rate ratio test, using the poisson.test function, and comparing, across two cohorts, the number of de novo variants per the number of callable bp assessed. When comparing TD probands versus SSC controls, we utilized a one-sided test (alternative = “greater”), given the prior evidence for the role of de novo mutations in TD and other neurodevelopmental disorders. However, we compared rates between TD cohorts with a two-sided test because we did not expect these rates to differ. In secondary burden analyses, one-sided binomial exact tests (binom.test) and Fisher’s exact tests (fisher.test), as well as a Poisson regression (see “Poisson Regression”) also assessed significance.
