The preceding analysis can be extended to carry out per strand and per phenotype tests if required. The script would need amending to introduce strand information in the ASESet object construction step. Doing so usually requires that the RNAseq experiment and alignment steps were performed with strandedness in mind and the bioinformatics pipeline up to here configured accordingly. Phenotype information can be added in the construction step using the colData parameter and a vector of phenotype or sample types for columns in the ASESet object.