pruneIntervals: Prune nested k-mer intervals from called k-mer peak set.

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

Description

Every k-mer identified by SArKS is derived as a substring defined by the interval running position i to position i+k-1 of the concatenation of all input sequences. In some cases a j-mer (with j < k) may be separately identified as a peak by SArKS for which the j-mer interval is entirely contained within [i, i+k-1]; this function removes such nested intervals from the reported collection of peaks.

Usage

pruneIntervals(intervals, start = "s", end = NULL)

Arguments

intervals	data.frame containing called k-mer peaks information (format as output from kmerPeaks function).
start	name of column in intervals data.frame containing interval start coordinates
end	name of column in interval data.frame containing interval end coordinates; if no such column present, default NULL value indicates that end coordinates should be obtained by adding nchar(intervals$kmer) to the start coordinates to obtain end coordinates.

Value

modified data.frame containing called k-mer peaks information (format as output from kmerPeaks function).

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)
peaks <- kmerPeaks(sarks, filters, thresholds)
prunedPeaks <- pruneIntervals(peaks)

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