55 lines
1.9 KiB
R
55 lines
1.9 KiB
R
#
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#options(warn=2)
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#options(error=recover)
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#
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HALF = high_dimensional_integrate(1, -200, 0, dnorm)
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print(paste("Should be ~ HALF: ", HALF, sep=""))
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k = 75
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#theta = 10^-2
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theta = 10^-3
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p = pHetPairLteDistance(k, theta)
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print(paste(p, " = pHetPairLteDistance(k= ", k, ", theta= ", theta, ")", sep=""))
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L = 76
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fragmentSize = 452
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p = pPairedEndReadsOfSpecificFragmentCanCoverHetPairAtDistance(L, fragmentSize, k)
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print(paste(p, " = pPairedEndReadsOfSpecificFragmentCanCoverHetPairAtDistance(L= ", L, ", fragmentSize= ", fragmentSize, ", k= ", k, ")", sep=""))
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Fm = 392
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Fs = 44
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p = pFragmentSize(300, Fm, Fs)
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print(paste(p, " = pFragmentSize(300, Fm= ", Fm, ", Fs= ", Fs, ")", sep=""))
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p = pFragmentsReadsCanCoverHetPairAtDistance(L, k, Fm, Fs)
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print(paste(p, " = pFragmentsReadsCanCoverHetPairAtDistance(L= ", L, ", k= ", k, ", Fm= ", Fm, ", Fs= ", Fs, ")", sep=""))
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meanDepth = 65
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nReadsToPhase = 1
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p = pDirectlyPhaseHetPairAtDistanceUsingDepth(meanDepth, nReadsToPhase, L, k, Fm, Fs)
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print(paste(p, " = pDirectlyPhaseHetPairAtDistanceUsingDepth(meanDepth= ", meanDepth, ", nReadsToPhase= ", nReadsToPhase, ", L= ", L, ", k= ", k, ", Fm= ", Fm, ", Fs= ", Fs, ")", sep=""))
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p = pDirectlyPhaseHetPair(meanDepth, nReadsToPhase, L, theta, Fm, Fs)
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print(paste(p, " = pDirectlyPhaseHetPair(meanDepth= ", meanDepth, ", nReadsToPhase= ", nReadsToPhase, ", L= ", L, ", theta= ", theta, ", Fm= ", Fm, ", Fs= ", Fs, ")", sep=""))
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windowDistances = c(100, 100, 100, 100, 100)
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phaseIndex = 2
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p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Fm, Fs)
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print(paste(p, " = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances= (", paste(windowDistances, collapse=", "), "), phaseIndex= ", phaseIndex, ", meanDepth= ", meanDepth, ", nReadsToPhase= ", nReadsToPhase, ", L= ", L, ", Fm= ", Fm, ", Fs= ", Fs, ")", sep=""))
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traceback()
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warnings()
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