ggruenhagen3/coselenss: COnditional SELection on the Excess of NonSynonymous Substitutions

Tests for significant differences in selection between two groups of individuals. It makes extensive use of the dndscv R package. In short, the dndscv method estimates the number of nonsynonymous mutations that would be expected in the absence of selection by combining a nucleotide substitution model (196 rates encompassing all possible substitutions in each possible trinucleotide context, estimated from synonymous mutations in the dataset) and a set of genomic covariates which greatly improve the performance of the method at low mutation loads. Then, dn/ds is calculated as the ratio between the observed number of nonsynonymous mutations (n_obs) and its neutral expectation (n_exp). Finally, the significance of dn/ds is computed through a likelihood ratio test, where the null hypothesis corresponds to dn/ds=1.

install.packages("remotes")
remotes::install_github("ggruenhagen3/coselenss")