permutationThresholds {sarks} | R Documentation |
Calculate thresholds for SArKS k-mer calling from permutation distribution.
permutationThresholds(filters, permDist, nSigma = 4)
filters |
output from sarksFilters function indicating what combinations of filter parameters halfWindow, spatialLength, and minGini to use. |
permDist |
output from permutationDistribution function. |
nSigma |
number of standard deviations above mean of permutation distribution at which to set threshold for either windowed or spatially-windowed score. |
named list with two elements: ‘theta’ containing a data.frame with the threshold information and ‘.java’ containing an R representation of the java object with 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) thresholds <- permutationThresholds(filters, permDist, nSigma=2.0)