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

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Documentation for package ‘sarks’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

blockInfo	Get sarks smoothed scores for input sequence
blockScores	SArKS input scores
clusterCounts	Count occurrences of k-mer clusters
clusterKmers	Cluster k-mers
estimateFalsePositiveRate	Estimating SArKS false positive rate
extendKmers	Extend k-mers in length where possible
kmerCounts	Count occurrences of k-mer
kmerPeaks	Call k-mer peaks
locateClusters	Locate occurrences of specified clusters of k-mers
locateKmers	Locate occurrences of specified k-mers
mergedKmerSubPeaks	Identify and merge k-mer sub-peaks within multi-motif domains
permutationDistribution	Estimating distribution of maximum smoothed sequence scores under permutation
permutationThresholds	Set smoothed score thresholds based on permutation distribution
pruneIntervals	Prune nested k-mer intervals from called k-mer peak set.
regexCounts	Count occurrences of regular expression
regexLocate	Locate occurrences of regular expression
Sarks	Suffix Array Kernel Smoothing
sarksFilters	Smoothing window and Gini impurity filter settings
simulatedScores	Scores associated with simulated sequences from SArKS paper.
simulatedSeqs	Simulated sequences from SArKS paper.
sourceBlock	Identify associated input sequence for given position(s) in suffix array