48 lines
1.7 KiB
R
48 lines
1.7 KiB
R
theta = 10^-3
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L = 101
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meanDepth = 65
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nReadsToPhase = 1
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params = paste("meanDepth= ", meanDepth, ", nReadsToPhase= ", nReadsToPhase, ", L= ", L, ", theta= ", theta, sep="")
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MEAN_SIZES = seq(1,2000,20)
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STD_SIZES = seq(0,200,5)
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testFragments = matrix(nrow=length(MEAN_SIZES), ncol=length(STD_SIZES))
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for (i in 1:length(MEAN_SIZES)) {
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test_mean_fragment_size = MEAN_SIZES[i]
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print(paste("test_mean_fragment_size: ", test_mean_fragment_size, sep=""))
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for (j in 1:length(STD_SIZES)) {
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test_std_fragment_size = STD_SIZES[j]
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print(paste("test_std_fragment_size: ", test_std_fragment_size, sep=""))
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testFragments[i,j] = pDirectlyPhaseHetPair(meanDepth, nReadsToPhase, L, theta, test_mean_fragment_size, test_std_fragment_size)
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}
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}
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pdf('testFragments.pdf')
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library(gplots)
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heatmap.2(testFragments, ylab = "Mean fragment size", xlab = "Standard deviation fragment size", labRow = MEAN_SIZES, labCol = STD_SIZES, Rowv = NA, Colv = NA, dendrogram = "none", scale="none", revC = FALSE, density.info="none", trace="none", main=params)
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library(scatterplot3d)
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xMeans = as.vector(t(matrix(rep.int(MEAN_SIZES, length(STD_SIZES)), ncol = length(STD_SIZES))))
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yStds = rep.int(STD_SIZES, length(MEAN_SIZES))
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zPhaseRate = as.vector(t(testFragments))
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scatterplot3d(xMeans, yStds, zPhaseRate, xlab = "Mean fragment size", ylab = "Standard deviation fragment size", zlab = "Phasing rate", main=params)
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bestCombo = which.max(zPhaseRate)
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print(paste("For ", params, ", BEST choice gives phaseability of ", zPhaseRate[bestCombo], " using mean fragment = ", xMeans[bestCombo], ", std. fragment = ", yStds[bestCombo], sep = ""))
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dev.off()
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save(list = ls(all=TRUE), file = "testFragments.RData")
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