Nothing
test_Sarks <- function() {
data(simulatedSeqs, simulatedScores)
sarks <- Sarks(simulatedSeqs, simulatedScores, 4, 0, 1)
yhat <- sarks$getYhat()
checkEquals(length(yhat), 7530)
checkEqualsNumeric(median(yhat), 1/3, tolerance=1e-6)
checkEqualsNumeric(max(yhat), 1, tolerance=1e-6)
}
test_permutationDistribution <- function() {
data(simulatedSeqs, simulatedScores)
sarks <- Sarks(simulatedSeqs, simulatedScores, 4, 0, 1)
filters <- sarksFilters(halfWindow=4, spatialLength=0, minGini=1.1)
permDist <- permutationDistribution(sarks, 20, filters, seed=123)
checkTrue(is.data.frame(permDist$windowed))
checkTrue(!any(is.na(permDist$windowed$max)))
checkTrue(max(permDist$windowed$max) <= 1 + 1e-6)
}
test_kmerPeaks <- function() {
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)
checkTrue(all(grepl('TACTGA', peaks$kmer)))
}
test_mergedKmerSubPeaks <- function() {
data(simulatedSeqs, simulatedScores)
sarks <- Sarks(simulatedSeqs, simulatedScores, 4, 3, 1)
filters <- sarksFilters(halfWindow=4, spatialLength=3, minGini=1.1)
permDist <- permutationDistribution(sarks, 250, filters, seed=123)
thresholds <- permutationThresholds(filters, permDist, nSigma=4.0)
mergedSubPeaks <- mergedKmerSubPeaks(sarks, filters, thresholds)
checkTrue(all(grepl('CTGAG', mergedSubPeaks$kmer)))
}
test_clusterKmers <- function() {
kmers <- c(
'CAGCCTGG', 'CCTGGAA', 'CAGCCTG', 'CCTGGAAC', 'CTGGAACT',
'ACCTGC', 'CACCTGC', 'TGGCCTG', 'CACCTG', 'TCCAGC',
'CTGGAAC', 'CACCTGG', 'CTGGTCTA', 'GTCCTG', 'CTGGAAG', 'TTCCAGC'
)
kmcl <- clusterKmers(kmers, directional=FALSE)
clLens <- vapply(kmcl, length, 0)
checkEquals(length(kmcl), 6)
checkEquals(max(clLens), 7)
}
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