Mercurial > repos > devteam > dwt_var_perfeature

annotate execute_dwt_var_perFeature.R @ 3:6c29c7e347e8 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:34:27 -0400
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6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 #####################################################################
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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2 ## plot multiscale wavelet variance
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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3 ## create null bands by permuting the original data series
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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4 ## generate plots and table of wavelet variance including p-values
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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5 #######################################################################
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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6 options(echo = FALSE)
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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7 library("wavethresh");
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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8 library("waveslim");
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 library("bitops");
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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10
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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11 ## to determine if data is properly formatted 2^N observations
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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12 is_power2 <- function(x) {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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13 x && !(bitops::bitAnd(x, x - 1));
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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14 }
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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16 ## dwt : discrete wavelet transform using Haar wavelet filter, simplest wavelet function but later can modify to let user-define the wavelet filter function
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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17 dwt_var_permut_get_max <- function(data, names, alpha, filter = 1, family = "DaubExPhase", bc = "symmetric", method = "kendall", wf = "haar", boundary = "reflection") {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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18 title <- NULL;
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19 final_pvalue <- NULL;
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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20 j <- NULL;
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21 scale <- NULL;
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22 out <- NULL;
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24 print(class(data));
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25 print(names);
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26 print(alpha);
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28 par(mar = c(5, 4, 4, 3), oma = c(4, 4, 3, 2), xaxt = "s", cex = 1, las = 1);
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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30 title <- c("Wavelet", "Variance", "Pvalue", "Test");
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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31 print(title);
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32
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33 for (i in seq_len(length(names))) {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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34 temp <- NULL;
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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35 results <- NULL;
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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36 wave1_dwt <- NULL;
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37
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38 ## if data fails formatting check, do something
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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39 print(is.numeric(as.matrix(data)[, i]));
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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40 if (!is.numeric(as.matrix(data)[, i])) {
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41 stop("data must be a numeric vector");
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42 }
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43 print(length(as.matrix(data)[, i]));
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44 print(is_power2(length(as.matrix(data)[, i])));
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45 if (!is_power2(length(as.matrix(data)[, i]))) {
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46 stop("data length must be a power of two");
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47 }
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48 j <- wavethresh::wd(as.matrix(data)[, i], filter.number = filter, family = family, bc = bc)$nlevels;
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49 print(j);
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50 temp <- vector(length = j);
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51 wave1_dwt <- waveslim::dwt(as.matrix(data)[, i], wf = wf, j, boundary = boundary);
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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52
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53 temp <- waveslim::wave.variance(wave1_dwt)[- (j + 1), 1];
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54 print(temp);
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55
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56 ##permutations code :
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57 feature1 <- NULL;
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58 null <- NULL;
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59 var_lower <- NULL;
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60 limit_lower <- NULL;
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61 var_upper <- NULL;
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62 limit_upper <- NULL;
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63 med <- NULL;
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64
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65 limit_lower <- alpha / 2 * 1000;
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66 print(limit_lower);
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67 limit_upper <- (1 - alpha / 2) * 1000;
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68 print(limit_upper);
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69
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70 feature1 <- as.matrix(data)[, i];
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71 for (k in 1:1000) {
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72 nk_1 <- NULL;
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73 null_levels <- NULL;
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74 var <- NULL;
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75 null_wave1 <- NULL;
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76
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77 nk_1 <- sample(feature1, length(feature1), replace = FALSE);
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78 null_levels <- wavethresh::wd(nk_1, filter.number = filter, family = family, bc = bc)$nlevels;
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79 var <- vector(length = length(null_levels));
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80 null_wave1 <- waveslim::dwt(nk_1, wf = wf, j, boundary = boundary);
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81 var <- waveslim::wave.variance(null_wave1)[- (null_levels + 1), 1];
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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82 null <- rbind(null, var);
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83 }
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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84 null <- apply(null, 2, sort, na.last = TRUE);
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85 var_lower <- null[limit_lower, ];
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86 var_upper <- null[limit_upper, ];
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87 med <- (apply(null, 2, median, na.rm = TRUE));
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88
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89 ## plot
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90 results <- cbind(temp, var_lower, var_upper);
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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91 print(results);
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92 matplot(results, type = "b", pch = "*", lty = 1, col = c(1, 2, 2), xaxt = "n", xlab = "Wavelet Scale", ylab = "Wavelet variance");
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93 mtext(names[i], side = 3, line = 0.5, cex = 1);
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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94 axis(1, at = 1:j, labels = c(2 ^ (0:(j - 1))), las = 3, cex.axis = 1);
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95
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96 ## get pvalues by comparison to null distribution
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97 for (m in seq_len(length(temp))) {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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98 print(paste("scale", m, sep = " "));
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99 print(paste("var", temp[m], sep = " "));
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100 print(paste("med", med[m], sep = " "));
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101 pv <- NULL;
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102 tail <- NULL;
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103 scale <- NULL;
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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104 scale <- 2 ^ (m - 1);
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105 if (temp[m] >= med[m]) {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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106 ## R tail test
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107 print("R");
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108 tail <- "R";
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109 pv <- (length(which(null[, m] >= temp[m]))) / (length(na.exclude(null[, m])));
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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110 } else {
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111 if (temp[m] < med[m]) {
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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112 ## L tail test
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113 print("L");
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114 tail <- "L";
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115 pv <- (length(which(null[, m] <= temp[m]))) / (length(na.exclude(null[, m])));
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116 }
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117 }
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118 print(pv);
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119 out <- rbind(out, c(paste("Scale", scale, sep = "_"), format(temp[m], digits = 3), pv, tail));
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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120 }
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121 final_pvalue <- rbind(final_pvalue, out);
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122 }
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123 colnames(final_pvalue) <- title;
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124 return(final_pvalue);
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125 }
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126
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127 ## execute
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128 ## read in data
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129 args <- commandArgs(trailingOnly = TRUE)
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130
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131 data_test <- NULL;
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132 final <- NULL;
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133 sub <- NULL;
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134 sub_names <- NULL;
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135 data_test <- read.delim(args[1], header = FALSE);
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136 pdf(file = args[5], width = 11, height = 8)
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137 for (f in strsplit(args[2], ",")) {
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138 f <- as.integer(f)
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139 if (f > ncol(data_test))
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140 stop(paste("column", f, "doesn't exist"));
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141 sub <- data_test[, f];
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142 sub_names <- colnames(data_test)[f];
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143 final <- rbind(final, dwt_var_permut_get_max(sub, sub_names, as.double(args[3])));
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144 }
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145
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146 dev.off();
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147 write.table(final, file = args[4], sep = "\t", quote = FALSE, row.names = FALSE);