For each of these 27 combinations, we computed the mutant-frequency distribution for selection coefficients of 0, ±0.001, ±0.01, ±0.1, ±0.3, and ±0.5 and no mutation.
Given a gene and its associated neighborhoods containing binding sites of main factors and a cofactor involved in a TF combination, we computed a feature score to quantify the association strength between the TF combination and the gene (see Methods).
For each such combination, we compute a T2 value and p-value as noted above, and we also assign a weight proportional to the product of the probabilities of inclusion (exclusion) used.
Moreover, for each combination of technologies, we computed the sets of B. fulgida ORFs with mapping above a given threshold, by varying this threshold as described above.
To estimate performance of pairwise combinations of our four models we computed the number of peaks with BSs recognized by each pairs of models.
We computed the latter from our 35 normal genomes by pairing them in all possible (595) combinations, computing our measures of repeat incidence and variability for each pair, and pooling the resulting data.
To assess the optimal non-linear combination of attributes we compute the nonadditive set functions μ, and using them, we determine the impact of individual mutations, both activating and inactivating, by computing the AHD as in [ Eq. (1 )].
In each run, for each combination of levels we compute the R of the RSR prediction with the outcome and the R of the RR prediction with the outcome.
As for homozygous allele combinations, we compute (7) To get shares of u and v, we can combine z with counts of AA and BB.
