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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 18:12:29 +0000
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509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 ###########################################################################################
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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2 ## code to do wavelet Indel vs. Control
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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3 ## signal is the difference I-C; function is second moment i.e. variance from zero not mean
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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4 ## to perform wavelet transf. of signal, scale-by-scale analysis of the function
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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5 ## create null bands by permuting the original data series
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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6 ## generate plots and table matrix of correlation coefficients including p-values
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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7 ############################################################################################
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8 library("wavethresh");
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 library("waveslim");
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10
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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11 options(echo = FALSE)
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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12
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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13 ## normalize data
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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14 norm <- function(data) {
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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15 v <- (data - mean(data)) / sd(data);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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16 if (sum(is.na(v)) >= 1) {
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17 v <- data;
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18 }
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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19 return(v);
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20 }
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509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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22 dwt_cor <- function(data_short, names_short, data_long, names_long, test, pdf, table, filter = 4, bc = "symmetric", wf = "haar", boundary = "reflection") {
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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23 print(test);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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24 print(pdf);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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25 print(table);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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26
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27 pdf(file = pdf);
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28 final_pvalue <- NULL;
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29 title <- NULL;
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31 short_levels <- wavethresh::wd(data_short[, 1], filter.number = filter, bc = bc)$nlevels;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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32 title <- c("motif");
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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33 for (i in 1:short_levels) {
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34 title <- c(title, paste(i, "moment2", sep = "_"), paste(i, "pval", sep = "_"), paste(i, "test", sep = "_"));
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35 }
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36 print(title);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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37
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38 ## loop to compare a vs a
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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39 for (i in seq_len(length(names_short))) {
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40 wave1_dwt <- NULL;
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41 m2_dwt <- NULL;
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42 diff <- NULL;
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43 var_dwt <- NULL;
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44 out <- NULL;
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45 out <- vector(length = length(title));
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46
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47 print(names_short[i]);
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48 print(names_long[i]);
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49
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50 ## need exit if not comparing motif(a) vs motif(a)
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51 if (names_short[i] != names_long[i]) {
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52 stop(paste("motif", names_short[i], "is not the same as", names_long[i], sep = " "));
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53 }
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54 else {
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55 ## signal is the difference I-C data sets
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56 diff <- data_short[, i] - data_long[, i];
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57
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58 ## normalize the signal
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59 diff <- norm(diff);
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60
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61 ## function is 2nd moment
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62 ## 2nd moment m_j = 1/N[sum_N(W_j + V_J)^2] = 1/N sum_N(W_j)^2 + (X_bar)^2
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63 wave1_dwt <- waveslim::dwt(diff, wf = wf, short_levels, boundary = boundary);
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64 var_dwt <- waveslim::wave.variance(wave1_dwt);
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65 m2_dwt <- vector(length = short_levels)
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66 for (level in 1:short_levels) {
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67 m2_dwt[level] <- var_dwt[level, 1] + (mean(diff)^2);
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68 }
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69
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70 ## CI bands by permutation of time series
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71 feature1 <- NULL;
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72 feature2 <- NULL;
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73 feature1 <- data_short[, i];
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74 feature2 <- data_long[, i];
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75 null <- NULL;
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76 results <- NULL;
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77 med <- NULL;
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78 m2_25 <- NULL;
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79 m2_975 <- NULL;
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80
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81 for (k in 1:1000) {
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82 nk_1 <- NULL;
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83 nk_2 <- NULL;
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84 m2_null <- NULL;
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85 var_null <- NULL;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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86 null_levels <- NULL;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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87 null_wave1 <- NULL;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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88 null_diff <- NULL;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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89 nk_1 <- sample(feature1, length(feature1), replace = FALSE);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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90 nk_2 <- sample(feature2, length(feature2), replace = FALSE);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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91 null_levels <- wavethresh::wd(nk_1, filter.number = filter, bc = bc)$nlevels;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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92 null_diff <- nk_1 - nk_2;
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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93 null_diff <- norm(null_diff);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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94 null_wave1 <- waveslim::dwt(null_diff, wf = wf, short_levels, boundary = boundary);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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95 var_null <- waveslim::wave.variance(null_wave1);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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96 m2_null <- vector(length = null_levels);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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97 for (level in 1:null_levels) {
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98 m2_null[level] <- var_null[level, 1] + (mean(null_diff)^2);
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99 }
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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100 null <- rbind(null, m2_null);
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101 }
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102
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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103 null <- apply(null, 2, sort, na.last = TRUE);
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104 m2_25 <- null[25, ];
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105 m2_975 <- null[975, ];
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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106 med <- apply(null, 2, median, na.rm = TRUE);
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107
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108 ## plot
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109 results <- cbind(m2_dwt, m2_25, m2_975);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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110 matplot(results, type = "b", pch = "*", lty = 1, col = c(1, 2, 2), xlab = "Wavelet Scale", ylab = c("Wavelet 2nd Moment", test), main = (names_short[i]), cex.main = 0.75);
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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111 abline(h = 1);
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112
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113 ## get pvalues by comparison to null distribution
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114 out <- c(names_short[i]);
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115 for (m in seq_len(length(m2_dwt))) {
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116 print(paste("scale", m, sep = " "));
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117 print(paste("m2", m2_dwt[m], sep = " "));
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118 print(paste("median", med[m], sep = " "));
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119 out <- c(out, format(m2_dwt[m], digits = 4));
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120 pv <- NULL;
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121 if (is.na(m2_dwt[m])) {
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122 pv <- "NA";
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123 }
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124 else {
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125 if (m2_dwt[m] >= med[m]) {
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126 ## R tail test
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127 tail <- "R";
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128 pv <- (length(which(null[, m] >= m2_dwt[m]))) / (length(na.exclude(null[, m])));
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129 }
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130 else{
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131 if (m2_dwt[m] < med[m]) {
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132 ## L tail test
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133 tail <- "L";
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134 pv <- (length(which(null[, m] <= m2_dwt[m]))) / (length(na.exclude(null[, m])));
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135 }
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136 }
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137 }
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138 out <- c(out, pv);
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139 print(pv);
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140 out <- c(out, tail);
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141 }
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142 final_pvalue <- rbind(final_pvalue, out);
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143 print(out);
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144 }
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145 }
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146
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147 colnames(final_pvalue) <- title;
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148 write.table(final_pvalue, file = table, sep = "\t", quote = FALSE, row.names = FALSE);
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149 dev.off();
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150 }
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151 ## execute
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152 ## read in data
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153 args <- commandArgs(trailingOnly = TRUE)
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154
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155 input_data <- read.delim(args[1]);
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156 input_data_names <- colnames(input_data);
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157
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158 control_data <- read.delim(args[2]);
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159 control_data_names <- colnames(control_data);
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160
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161 ## call the test function to implement IvC test
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162 dwt_cor(input_data, input_data_names, control_data, control_data_names, test = "IvC", pdf = args[3], table = args[4]);
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163 print("done with the correlation test");