mergedKmerSubPeaks: Identify and merge k-mer sub-peaks within multi-motif domains

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

Description

When spatials smoothing is employed, SArKS identifies spatial windows containing elevated spatially-averaged sequence-smoothed scores (multi-motif domains, or MMDs). This function finds k-mers within these MMDs whose sequence-smoothed scores are above the threshold used for MMD calling and merges such k-mers when their spatial positions overlap.

Usage

mergedKmerSubPeaks(sarks, filters, thresholds, peakify = TRUE,
    kMax = 12L)

Arguments

sarks	Sarks object to use for k-mer peak calling.
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.
peakify	logical value specifying whether to restrict initial k-mer peak calling to only spatial positions at which the smoothed score is at least as high as either neighboring position (or not).
kMax	integer value indicating the maximum k-mer length for initial k-mer peak calling.

Value

data.frame containing called k-mer peak information.

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, 3, 1)
filters <- sarksFilters(halfWindow=4, spatialLength=3, minGini=1.1)
permDist <- permutationDistribution(sarks, 250, filters, seed=123)
thresholds <- permutationThresholds(filters, permDist, nSigma=4.0)
mergedSubPeaks <- mergedKmerSubPeaks(sarks, filters, thresholds)

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