Mercurial > repos > devteam > dwt_cor_ava_perclass

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:28:54 -0400
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 ##################################################################################
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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2 ## code to do all correlation tests of form: motif(a) vs. motif(a)
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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3 ## add code to create null bands by permuting the original data series
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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4 ## generate plots and table matrix of correlation coefficients including p-values
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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5 ##################################################################################
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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6 library("wavethresh");
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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7 library("waveslim");
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 options(echo = FALSE)
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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11 ## normalize data
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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12 norm <- function(data) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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13 v <- (data - mean(data)) / sd(data);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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14 if (sum(is.na(v)) >= 1) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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15 v <- data;
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16 }
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17 return(v);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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18 }
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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20 dwt_cor <- function(data_short, names_short, data_long, names_long, test, pdf, table, filter = 4, bc = "symmetric", method = "kendall", wf = "haar", boundary = "reflection") {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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21 print(test);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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22 print(pdf);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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23 print(table);
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25 pdf(file = pdf);
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26 final_pvalue <- NULL;
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27 title <- NULL;
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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29 short_levels <- wavethresh::wd(data_short[, 1], filter.number = filter, bc = bc)$nlevels;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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30 title <- c("motif");
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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31 for (i in 1:short_levels) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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32 title <- c(title, paste(i, "cor", sep = "_"), paste(i, "pval", sep = "_"));
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33 }
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34 print(title);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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36 ## normalize the raw data
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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37 data_short <- apply(data_short, 2, norm);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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38 data_long <- apply(data_long, 2, norm);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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39
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40 for (i in seq_len(length(names_short))) {
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41 ## Kendall Tau
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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42 ## DWT wavelet correlation function
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43 ## include significance to compare
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44 wave1_dwt <- NULL;
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45 wave2_dwt <- NULL;
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46 tau_dwt <- NULL;
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47 out <- NULL;
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48
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49 print(names_short[i]);
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50 print(names_long[i]);
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51
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52 ## need exit if not comparing motif(a) vs motif(a)
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53 if (names_short[i] != names_long[i]) {
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54 stop(paste("motif", names_short[i], "is not the same as", names_long[i], sep = " "));
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55 }
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56 else {
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57 wave1_dwt <- waveslim::dwt(data_short[, i], wf = wf, short_levels, boundary = boundary);
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58 wave2_dwt <- waveslim::dwt(data_long[, i], wf = wf, short_levels, boundary = boundary);
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59 tau_dwt <- vector(length = short_levels)
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60
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61 ## perform cor test on wavelet coefficients per scale
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62 for (level in 1:short_levels) {
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63 w1_level <- NULL;
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64 w2_level <- NULL;
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65 w1_level <- (wave1_dwt[[level]]);
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66 w2_level <- (wave2_dwt[[level]]);
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67 tau_dwt[level] <- cor.test(w1_level, w2_level, method = method)$estimate;
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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 cor_25 <- NULL;
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79 cor_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;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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84 null_levels <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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85 cor <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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86 null_wave1 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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87 null_wave2 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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88
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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89 nk_1 <- sample(feature1, length(feature1), replace = FALSE);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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90 nk_2 <- sample(feature2, length(feature2), replace = FALSE);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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91 null_levels <- wavethresh::wd(nk_1, filter.number = filter, bc = bc)$nlevels;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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92 cor <- vector(length = null_levels);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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93 null_wave1 <- waveslim::dwt(nk_1, wf = wf, short_levels, boundary = boundary);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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94 null_wave2 <- waveslim::dwt(nk_2, wf = wf, short_levels, boundary = boundary);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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95
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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96 for (level in 1:null_levels) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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97 null_level1 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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98 null_level2 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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99 null_level1 <- (null_wave1[[level]]);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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100 null_level2 <- (null_wave2[[level]]);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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101 cor[level] <- cor.test(null_level1, null_level2, method = method)$estimate;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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102 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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103 null <- rbind(null, cor);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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104 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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105
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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106 null <- apply(null, 2, sort, na.last = TRUE);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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107 print(paste("NAs", length(which(is.na(null))), sep = " "));
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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108 cor_25 <- null[25, ];
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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109 cor_975 <- null[975, ];
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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110 med <- (apply(null, 2, median, na.rm = TRUE));
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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111
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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112 ## plot
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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113 results <- cbind(tau_dwt, cor_25, cor_975);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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114 matplot(results, type = "b", pch = "*", lty = 1, col = c(1, 2, 2), ylim = c(-1, 1), xlab = "Wavelet Scale", ylab = "Wavelet Correlation Kendall's Tau", main = (paste(test, names_short[i], sep = " ")), cex.main = 0.75);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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115 abline(h = 0);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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116
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117 ## get pvalues by comparison to null distribution
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118 ### modify pval calculation for error type II of T test ####
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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119 out <- (names_short[i]);
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120 for (m in seq_len(length(tau_dwt))) {
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121 print(paste("scale", m, sep = " "));
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122 print(paste("tau", tau_dwt[m], sep = " "));
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123 print(paste("med", med[m], sep = " "));
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124 out <- c(out, format(tau_dwt[m], digits = 3));
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125 pv <- NULL;
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126 if (is.na(tau_dwt[m])) {
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127 pv <- "NA";
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128 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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129 else {
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130 if (tau_dwt[m] >= med[m]) {
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131 ## R tail test
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132 print(paste("R"));
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133 ### per sv ok to use inequality not strict
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134 pv <- (length(which(null[, m] >= tau_dwt[m]))) / (length(na.exclude(null[, m])));
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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135 if (tau_dwt[m] == med[m]) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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136 print("tau == med");
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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137 print(summary(null[, m]));
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138 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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139 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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140 else if (tau_dwt[m] < med[m]) {
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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141 ## L tail test
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142 print(paste("L"));
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143 pv <- (length(which(null[, m] <= tau_dwt[m]))) / (length(na.exclude(null[, m])));
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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144 }
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145 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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146 out <- c(out, pv);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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147 print(paste("pval", pv, sep = " "));
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148 }
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149 final_pvalue <- rbind(final_pvalue, out);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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150 print(out);
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151 }
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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152 }
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153 colnames(final_pvalue) <- title;
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154 write.table(final_pvalue, file = table, sep = "\\t", quote = FALSE, row.names = FALSE)
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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155 dev.off();
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156 }
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157 ## execute
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158 ## read in data
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159 args <- commandArgs(trailingOnly = TRUE)
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160
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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161 input_data1 <- NULL;
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162 input_data2 <- NULL;
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163 input_data_short1 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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164 input_data_short2 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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165 input_data_names_short1 <- NULL;
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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166 input_data_names_short2 <- NULL;
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167
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168 input_data1 <- read.delim(args[1]);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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169 input_data_short1 <- input_data1[, +c(seq_len(ncol(input_data1)))];
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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170 input_data_names_short1 <- colnames(input_data_short1);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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171
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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172 input_data2 <- read.delim(args[2]);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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173 input_data_short2 <- input_data2[, +c(seq_len(ncol(input_data2)))];
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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174 input_data_names_short2 <- colnames(input_data_short2);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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175
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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176 ## cor test for motif(a) in input_data1 vs motif(a) in input_data2
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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177 dwt_cor(input_data_short1, input_data_names_short1, input_data_short2, input_data_names_short2, test = "cor_aVa", pdf = args[3], table = args[4]);
b87bbe6bc044 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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178 print("done with the correlation test");