extendKmers {sarks} | R Documentation |
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).
extendKmers(sarks, sarksTable)
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). |
modified data.frame containing called k-mer peaks information (format as output from kmerPeaks function).
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) peaks <- kmerPeaks(sarks, filters, thresholds) prunedPeaks <- pruneIntervals(peaks) extendedPeaks <- extendKmers(sarks, prunedPeaks)