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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
author iuc
date Wed, 12 Jan 2022 19:07:45 +0000
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d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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1 ---
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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2 title: "Analysis by GenomicSuperSignature"
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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3 date: "`r Sys.Date()`"
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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4 output:
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5 BiocStyle::html_document:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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6 toc: true
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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7 toc_float: false
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8 toc_depth: 3
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9 params:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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10 val_all: val_all
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11 dat: dat
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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12 RAVmodel: RAVmodel
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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13 inputName: inputName
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14 numOut: numOut
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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15 ---
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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16
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17 ```{r setup, include=FALSE}
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18 knitr::opts_chunk$set(echo = FALSE)
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19 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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20
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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21 # RAVs best represents your dataset
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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22 The *validation* provides a quantitative representation of the relevance
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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23 between your dataset and RAVs. Below shows the top 6 validated RAVs and
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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24 the complete result is saved as `{input_name}_validate.csv`.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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25
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26 ```{r}
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27 head(params$val_all)
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28 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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29
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30 ## Heatmap Table
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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31 `heatmapTable` takes validation results as its input and displays them into
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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32 a two panel table: the top panel shows the average silhouette width (avg.sw)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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33 and the bottom panel displays the validation score.
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34
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35 `heatmapTable` can display different subsets of the validation output. For
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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36 example, if you specify `scoreCutoff`, any validation result above that score
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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37 will be shown. If you specify the number (n) of top validation results through
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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38 `num.out`, the output will be a n-columned heatmap table. You can also use the
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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39 average silhouette width (`swCutoff`), the size of cluster (`clsizecutoff`),
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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40 one of the top 8 PCs from the dataset (`whichPC`).
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41
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42 Here, we print out top `r params$numOut` validated RAVs with average silhouette
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43 width above 0.
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44
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45 ```{r out.height="45%", out.width="45%", message=FALSE, warning=FALSE}
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46 heatmapTable(params$val_all, num.out = params$numOut, swCutoff = 0)
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47 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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48
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49 ## Interactive Graph
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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50 Under the default condition, `plotValidate` plots validation results of all non
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51 single-element RAVs in one graph, where x-axis represents average silhouette
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52 width of the RAVs (a quality control measure of RAVs) and y-axis represents
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53 validation score. We recommend users to focus on RAVs with higher validation
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54 score and use average silhouette width as a secondary criteria.
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55
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56 ```{r out.height="80%", out.width="80%"}
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57 plotValidate(params$val_all, interactive = TRUE)
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58 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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59
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60 Note that `interactive = TRUE` will result in a zoomable, interactive plot that
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61 included tooltips, which is saved as `{input_name}_validate_plot.html` file.
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62
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63 You can hover each data point for more information:
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64
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65 - **sw** : the average silhouette width of the cluster
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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66 - **score** : the top validation score between 8 PCs of the dataset and RAVs
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67 - **cl_size** : the size of RAVs, represented by the dot size
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68 - **cl_num** : the RAV number. You need this index to find more information
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69 about the RAV.
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70 - **PC** : test dataset's PC number that validates the given RAV. Because we
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71 used top 8 PCs of the test dataset for validation, there are 8 categories.
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72
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73 If you double-click the PC legend on the right, you will enter an
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74 individual display mode where you can add an additional group of data
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75 point by single-click.
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76
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77
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78 # Prior information associated to your dataset
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79 ```{r echo=FALSE}
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80 validated_ind <- validatedSignatures(params$val_all, num.out = params$numOut,
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81 swCutoff = 0, indexOnly = TRUE)
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82
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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83 # In case, there are fewer validated_ind than the number of outputs user set
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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84 n <- min(params$numOut, length(validated_ind), na.rm = TRUE)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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85 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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86
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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87 ## MeSH terms in wordcloud
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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88 ```{r out.height="60%", out.width="60%", fig.width=8, fig.height=8}
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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89 for (i in seq_len(n)) {
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90 set.seed(1)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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91 print(paste0("MeSH terms related to RAV", validated_ind[i]))
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92 drawWordcloud(params$RAVmodel, validated_ind[i])
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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93 }
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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94 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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95
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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96 ## GSEA
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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97 The complete result is saved as `{input_name}_genesets_RAV*.csv`.
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98 ```{r}
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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99 res_all <- vector(mode = "list", length = n)
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100 for (i in seq_len(n)) {
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101 RAVnum <- validated_ind[i]
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102 RAVname <- paste0("RAV", RAVnum)
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103 res <- gsea(params$RAVmodel)[[RAVname]]
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104 res_all[[i]] <- head(res)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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105 names(res_all)[i] <- paste0("Enriched gene sets for RAV", validated_ind[i])
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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106 }
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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107 res_all
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108 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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109
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110 ## Publication
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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111 The complete result is saved as `{input_name}_literatures_RAV*.csv`.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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112 ```{r}
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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113 res_all <- vector(mode = "list", length = n)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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114 for (i in seq_len(n)) {
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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115 RAVnum <- validated_ind[i]
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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116 res <- findStudiesInCluster(params$RAVmodel, RAVnum, studyTitle = TRUE)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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117 res_all[[i]] <- head(res)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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118 names(res_all)[i] <- paste0("Studies related to RAV", validated_ind[i])
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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119 }
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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120 res_all
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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121 ```
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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122