31 lines
1.0 KiB
R
31 lines
1.0 KiB
R
L = 101
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Fm = 392
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Fs = 44
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meanDepth = 65
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nReadsToPhase = 1
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params = paste("meanDepth= ", meanDepth, ", nReadsToPhase= ", nReadsToPhase, ", L= ", L, ", Fm= ", Fm, ", Fs= ", Fs, sep="")
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distances = scan("~fromer/storage/phase.NA12878/COMPLETE_LIST.het_distances.txt", what=list(dist=0))
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distances = distances$dist
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MAX_NUM_DISTS = 10^4
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NUM_DISTS_TO_USE = min(MAX_NUM_DISTS, length(distances))
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distances = distances[1:NUM_DISTS_TO_USE]
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print(paste("Using ", NUM_DISTS_TO_USE, " EMPIRICAL distances...", sep=""))
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MAX_WINDOW_SIZE = 10
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FILE_NAME = "theoretical_window_on_empirical"
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phaseWindowResult = calcPhasingProbsForWindowDistances(distances, MAX_WINDOW_SIZE, meanDepth, nReadsToPhase, L, Fm, Fs, FILE_NAME)
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phaseProbsPositionWindow = phaseWindowResult$phaseProbsPositionWindow
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WINDOW_SIZES = phaseWindowResult$WINDOW_SIZES
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phaseProbsWindow = colMeans(phaseProbsPositionWindow)
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scatter(WINDOW_SIZES, phaseProbsWindow, FILE_NAME, xlab="Window size", ylab="Mean theoretical phasing rate on empirical distances", main=params, type="b")
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