The empirical P-value of a window was obtained as the percentage of statistics greater than its window average.
The same alignment was also analyzed with BRATNextGen (Marttinen et al. 2012), assuming four clusters, using a learned value of alpha, a window size of 1 kb, and a significance threshold P value of 0.05 (as calculated from 100 permutations).
Independently, the same whole genome alignment was analysed using BRATNextGen [ 55], assuming three clusters, using a learned value of alpha, a window size of one kilobase and a significance threshold P value of 0.05 (as calculated from 100 permutations).
Average value for a window of frames where tripod configurations = +1 value; tetrapod = −1; and noncanonical = 0. Standard deviation from the average point of adjacent ipsilateral footprints projected onto the displacement axis.
Sequences were trimmed further using SeqTrim v0.110 [ 58] with a minimum quality value of 20, a window size of 10 and no contamination removal step.
For all ChIP-chip experiments, in order to find promoter peaks, a maximum log-ratio value for a window consisting of three consecutive probes was determined for both experimental data and a random permutation of the data.
The other predictive feature described the mutation site environment as the mean, minimum, and maximum of the parameter values for a window of six neighbouring residues.
With this value of w, a window size s contributes 85% of the sum of the weights in an infinite window.
Briefly, sliding windows of four CpGs each were analyzed and the average value of all windows in a given region was used as an estimate of the ME of a given sample.
The second, extracted the percent signal change values for a windowed-average of the activity for the 4 s (2 imaging volumes; TR = 2) prior to movement (plan-epoch decoding).
