extendKmers: Extend k-mers in length where possible

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

Description

Extend k-mers when adding flanking characters from region in input sequence from which they are derived would result in another reported l-mer string (l > k).

Usage

extendKmers(sarks, sarksTable)

Arguments

sarks	Sarks object used to obtain k-mer peak call set.
sarksTable	data.frame containing called k-mer peaks information (format as output from kmerPeaks function).

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)
extendedPeaks <- extendKmers(sarks, prunedPeaks)

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