blockInfo {sarks} | R Documentation |
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).
blockInfo(sarks, block, filters, thresholds, kMax = 12L)
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. |
data.frame in same format as result of kmerPeaks giving detailed information about every spatial position within specified sequences/blocks.
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) bi24 <- blockInfo(sarks, '24', filters, thresholds)