estimateFalsePositiveRate: Estimating SArKS false positive rate

In sarks: Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Description

Run second 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, and comparing these values to thresholds determined by first round of permutation testing.

Usage

estimateFalsePositiveRate(sarks, reps, filters, thresholds, seed = NULL,
    conf.level = 0.95)

Arguments

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.
thresholds	output from permutationThresholds specifying thresholds for k-mer peak calling.
seed	optional seed for random number generator (use in case reproducibility of output is desired). NOTE: do not use the same seed passed to initial permutationDistribution call used to set thresholds.
conf.level	level of confidence to be used in the false positive rate confidence interval.

Value

named list with three elements: ‘permutation’ containing the output from permutationDistribution run.

References

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

Examples

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)
fpr <- estimateFalsePositiveRate(
        sarks, 250, filters, thresholds, seed=123456)

sarks documentation built on Nov. 8, 2020, 6:54 p.m.