Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_salience.R @ 7:ca9938f2eb6a draft default tip

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"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
author eschen42
date Tue, 17 Nov 2020 23:29:59 +0000
parents 0b49916c5c52
children
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50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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1 w4msalience <- function(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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2 data_matrix # a matrix of intensities; features as rows, and samples as columns
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3 , sample_class # a vector of sample class-levels; length(sample_class) == ncol(data_matrix)
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4 , failure_action = stop
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5 ) {
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6 library(stats)
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7 # begin sanity checks
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8 if ( !is.vector(sample_class) || !( is.character(sample_class) || is.factor(sample_class) ) ) {
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9 failure_action("w4msalience: Expected sample_class to be a vector of characters of factor-levels")
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10 return (NULL)
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11 }
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12 if ( !is.matrix(data_matrix) && !is.data.frame(data_matrix) ) {
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13 failure_action("w4msalience: Expected data_matrix to be a matrix (or data.frame) of numeric")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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14 return (NULL)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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15 }
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16 # transpose data_matrix so that columns are the features
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17 t_data_matrix <- t(data_matrix)
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18 if ( !is.matrix(t_data_matrix) || !is.numeric(t_data_matrix) ) {
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19 failure_action("w4msalience: Expected data_matrix to be a matrix (or data.frame) of numeric")
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20 return (NULL)
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21 }
7
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22
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23 feature_names <- colnames(t_data_matrix)
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24
0
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25 n_features <- ncol(t_data_matrix)
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26 n_samples <- nrow(t_data_matrix)
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27 if ( length(sample_class) != n_samples ) {
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28 strF(data_matrix)
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29 strF(sample_class)
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30 failure_action(
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31 sprintf(
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32 "w4msalience: The data_matrix has %d samples but sample_class has %d"
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33 , n_samples
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34 , length(sample_class)
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35 )
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36 )
0
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37 return (NULL)
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38 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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39 # end sanity checks
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40
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41 # "For each feature, 'select sample_class, median(intensity) from feature group by sample_class'."
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42 # The first column(s) of the result of aggregate has the classifier value(s) specified in the 'by' list.
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43 medianOfFeatureBySampleClassLevel <- aggregate(
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44 x = as.data.frame(t_data_matrix)
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45 , by = list(sample_class)
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46 , FUN = "median"
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47 )
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48
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49 # "For each feature, 'select sample_class, rcv(intensity) from feature group by sample_class'."
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50 # cv is less robust; deviation from normality degrades performance
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51 # cv(x) == sd(x) / mean(x)
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52 # rcv is a "robust" coefficient of variation, expressed as a proportion
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53 # rcv(x) == mad(x) / median(x)
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54 madOfFeatureBySampleClassLevel <- aggregate(
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55 x = as.data.frame(t_data_matrix)
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56 , by = list(sample_class)
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57 , FUN = "mad"
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58 )
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59
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60 # Note that `apply(X=array(1:10), MARGIN = 1, FUN = function(x) return(c(x,x^2)))`
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61 # produces a matrix with two rows and ten columns
0
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62
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63 my_list <- apply(
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64 X = array(1:n_features)
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65 , MARGIN = 1
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66 , FUN = function(x) {
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67 my_df <- data.frame(
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68 median = medianOfFeatureBySampleClassLevel[ , 1 + x]
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69 , mad = madOfFeatureBySampleClassLevel[ , 1 + x]
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70 )
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71 my_df$salient_level <- medianOfFeatureBySampleClassLevel[ , 1]
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72 my_df <- my_df[ order(my_df$median, decreasing = TRUE), ]
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73 my_dist_df <- my_df[ 1:2, ]
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74 # "robust coefficient of variation", i.e.,
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75 # mad(feature-intensity for class-level max_level) / median(feature-intensity for class-level max_level)
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76 rcv_result <- my_dist_df$mad[1] / my_dist_df$median[1]
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77 dist_result <-
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78 ( my_dist_df$median[1] - my_dist_df$median[2] ) /
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79 sqrt( my_dist_df$mad[1] * my_dist_df$mad[2] )
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80 if (is.infinite(dist_result) || is.nan(dist_result))
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81 dist_result <- 0
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82 mean_median <- mean(my_df$median)
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83 salience_result <- if (mean_median > 0) my_df$median[1] / mean_median else 0
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84 return (
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85 data.frame(
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86 dist_result = dist_result
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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87 , max_median = my_df$median[1]
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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88 , mean_median = mean_median
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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89 , salience_result = salience_result
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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90 , salient_level = my_df$salient_level[1]
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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91 , rcv_result = rcv_result
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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92 )
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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93 )
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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94 }
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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95 )
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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96 results_matrix <- sapply(X = 1:n_features, FUN = function(i) my_list[[i]])
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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97 results_df <- as.data.frame(t(results_matrix))
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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98
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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99 relative_salient_distance <- unlist(results_df$dist_result)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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100 salience <- unlist(results_df$salience_result)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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101 salient_level <- unlist(results_df$salient_level)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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102 max_median <- unlist(results_df$max_median)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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103 mean_median <- unlist(results_df$mean_median)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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104 rcv_result <- unlist(results_df$rcv_result)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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105
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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106 salience_df <-
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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107 data.frame(
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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108 # the feature name
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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109 feature = feature_names
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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110 # the name (or factor-level) of the class-level with the highest median intensity for the feature
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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111 , max_level = salient_level
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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112 # the median intensity for the feature and the level max_level
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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113 , max_median = max_median
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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114 # the distance between the maximum intensities for the feature at the two highest levels
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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115 , relative_salient_distance = relative_salient_distance
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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116 # the coefficient of variation (expressed as a proportion) for the intensity for the feature and the level max_level
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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117 , salience_rcv = rcv_result
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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118 # the mean of the medians of intensity for all class-levels for the feature
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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119 , mean_median = mean_median
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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120 # raw salience is the ratio of the most-prominent level to the mean of all levels for the feature
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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121 , salience = salience
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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122 # don't coerce strings to factors (this is a parameter for the data.frame constructor, not a column of the data.frame)
ca9938f2eb6a "planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
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123 , stringsAsFactors = FALSE
0
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124 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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125
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637
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126 return (salience_df)
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127 }
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128