permutationDistribution {sarks} | R Documentation |
Run permutation test using the specified number of repetitions, keeping track of maximum observed windowed and spatially-windowed smoothed scores for each combination of filter parameters for each permutation.
permutationDistribution(sarks, reps, filters, seed = NULL)
sarks |
Sarks object to test. |
reps |
integer specifying how many repetitions to test. |
filters |
output from sarksFilters function indicating what combinations of filter parameters halfWindow, spatialLength, and minGini to use. |
seed |
optional seed for random number generator (use in case reproducibility of output is desired). |
named list with three elements: ‘windowed’ containing a data.frame with the maximum smoothed scores for each permutation at each combination of filter parameter values, ‘spatial’ containing a data.frame with the maximum spatially-smoothed scores for each permutation and each filter parameter specification, and ‘.java’ containing the R representation of the java object encoding this information.
Wylie, D.C., Hofmann, H.A., and Zemelman, B.V. (2019) SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing, Bioinformatics, Vol. 35(20), 3944-3952
https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797
data(simulatedSeqs, simulatedScores) sarks <- Sarks(simulatedSeqs, simulatedScores, 4, 0, 1) filters <- sarksFilters(halfWindow=4, spatialLength=0, minGini=1.1) permDist <- permutationDistribution(sarks, 250, filters, seed=123)