blockInfo: Get sarks smoothed scores for input sequence

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

Description

Returns a data.frame containing the smoothed scores (including spatially smoothed scores, if applicable) as well as other useful sarks parameters for one or more specified input sequences (blocks).

Usage

blockInfo(sarks, block, filters, thresholds, kMax = 12L)

Arguments

sarks	Sarks object from which information will be derived.
block	character vector of names of sequence(s) for which results are desired
filters	output from sarksFilters function indicating what combinations of filter parameters halfWindow, spatialLength, and minGini were used.
thresholds	output from permutationThresholds specifying thresholds used for k-mer peak calling.
kMax	integer value indicating the maximum k-mer length to be reported.

Value

data.frame in same format as result of kmerPeaks giving detailed information about every spatial position within specified sequences/blocks.

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)
bi24 <- blockInfo(sarks, '24', filters, thresholds)

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