annotate mqppep_anova.R @ 0:8dfd5d2b5903 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
author galaxyp
date Mon, 11 Jul 2022 19:22:54 +0000
parents
children b76c75521d91
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8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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1 #!/usr/bin/env Rscript
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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2 # libraries
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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3 library(optparse)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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4 library(data.table)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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5 library(stringr)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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6
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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7 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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8
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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9 # parse options
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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10 option_list <- list(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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11 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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12 c("-i", "--inputFile"),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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13 action = "store",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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14 default = NA,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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15 type = "character",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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16 help = "Phosphopeptide Intensities sparse input file path"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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17 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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18 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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19 c("-a", "--alphaFile"),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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20 action = "store",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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21 default = NA,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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22 type = "character",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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23 help = paste0("List of alpha cutoff values for significance testing;",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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24 " path to text file having one column and no header")
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25 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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26 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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27 c("-S", "--preproc_sqlite"),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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28 action = "store",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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29 default = NA,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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30 type = "character",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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31 help = "Path to 'preproc_sqlite' produced by `mqppep_mrgfltr.py`"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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32 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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33 make_option(
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34 c("-K", "--ksea_sqlite"),
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35 action = "store",
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36 default = NA,
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37 type = "character",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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38 help = "Path to 'ksea_sqlite' output produced by this tool"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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39 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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40 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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41 c("-f", "--firstDataColumn"),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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42 action = "store",
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43 default = "^Intensity[^_]",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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44 type = "character",
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45 help = "First column of intensity values"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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46 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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47 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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48 c("-m", "--imputationMethod"),
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49 action = "store",
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50 default = "random",
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51 type = "character",
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52 help = paste0("Method for missing-value imputation,",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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53 " one of c('group-median','median','mean','random')")
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54 ),
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55 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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56 c("-p", "--meanPercentile"),
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57 action = "store",
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58 default = 3,
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59 type = "integer",
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60 help = paste0("Mean percentile for randomly generated imputed values;",
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61 ", range [1,99]")
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62 ),
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63 make_option(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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64 c("-d", "--sdPercentile"),
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65 action = "store",
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66 default = 3,
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67 type = "double",
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68 help = paste0("Adjustment value for standard deviation of",
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69 " randomly generated imputed values; real")
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70 ),
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71 make_option(
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72 c("-s", "--regexSampleNames"),
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73 action = "store",
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74 default = "\\.(\\d+)[A-Z]$",
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75 type = "character",
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76 help = "Regular expression extracting sample-names"
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77 ),
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78 make_option(
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79 c("-g", "--regexSampleGrouping"),
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80 action = "store",
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81 default = "(\\d+)",
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82 type = "character",
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83 help = paste0("Regular expression extracting sample-group",
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84 " from an extracted sample-name")
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parents:
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85 ),
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galaxyp
parents:
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86 make_option(
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parents:
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87 c("-o", "--imputedDataFile"),
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galaxyp
parents:
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88 action = "store",
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parents:
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89 default = "output_imputed.tsv",
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parents:
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90 type = "character",
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parents:
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91 help = "Imputed Phosphopeptide Intensities output file path"
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galaxyp
parents:
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92 ),
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parents:
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93 make_option(
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parents:
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94 c("-n", "--imputedQNLTDataFile"),
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parents:
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95 action = "store",
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96 default = "output_imp_qn_lt.tsv",
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97 type = "character",
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98 help =
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99 paste(
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100 "Imputed, Quantile-Normalized Log-Transformed Phosphopeptide",
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101 "Intensities output file path"
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102 )
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parents:
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103 ),
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104 make_option(
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105 c("-r", "--reportFile"),
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106 action = "store",
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107 default = "QuantDataProcessingScript.html",
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108 type = "character",
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parents:
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109 help = "HTML report file path"
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110 ),
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111 make_option(
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112 c("-k", "--ksea_cutoff_statistic"),
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113 action = "store",
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114 default = "FDR",
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115 type = "character",
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116 help = paste0("Method for missing-value imputation,",
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parents:
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117 " one of c('FDR','p.value'), but don't expect 'p.value' to work well.")
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118 ),
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119 make_option(
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120 c("-t", "--ksea_cutoff_threshold"),
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121 action = "store",
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parents:
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122 default = 0.05,
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galaxyp
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123 type = "double",
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124 help = paste0("Maximum score to be used to score a kinase enrichment as significant")
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125 ),
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126 make_option(
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127 c("-M", "--anova_ksea_metadata"),
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128 action = "store",
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129 default = "anova_ksea_metadata.tsv",
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130 type = "character",
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parents:
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131 help = "Phosphopeptide metadata, ANOVA FDR, and KSEA enribhments"
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132 )
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133 )
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134 args <- parse_args(OptionParser(option_list = option_list))
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135 print("args is:")
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136 cat(str(args))
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137
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138 # Check parameter values
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139
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galaxyp
parents:
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140 if (! file.exists(args$inputFile)) {
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galaxyp
parents:
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141 stop((paste("Input file", args$inputFile, "does not exist")))
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142 }
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parents:
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143 input_file <- args$inputFile
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144 alpha_file <- args$alphaFile
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145 preproc_sqlite <- args$preproc_sqlite
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146 imputed_data_file_name <- args$imputedDataFile
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parents:
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147 imp_qn_lt_data_filenm <- args$imputedQNLTDataFile
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148 anova_ksea_metadata <- args$anova_ksea_metadata
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149 report_file_name <- args$reportFile
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150 ksea_sqlite <- args$ksea_sqlite
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151 ksea_cutoff_statistic <- args$ksea_cutoff_statistic
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152 ksea_cutoff_threshold <- args$ksea_cutoff_threshold
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153 if (
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diff changeset
154 sum(
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galaxyp
parents:
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155 grepl(
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156 pattern = ksea_cutoff_statistic,
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157 x = c("FDR", "p.value")
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158 )
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159 ) < 1
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160 ) {
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161 print(sprintf("bad ksea_cutoff_statistic argument: %s", ksea_cutoff_statistic))
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162 return(-1)
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163 }
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164
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165 imputation_method <- args$imputationMethod
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166 if (
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parents:
diff changeset
167 sum(
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galaxyp
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168 grepl(
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169 pattern = imputation_method,
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170 x = c("group-median", "median", "mean", "random")
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171 )
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172 ) < 1
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173 ) {
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174 print(sprintf("bad imputationMethod argument: %s", imputation_method))
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175 return(-1)
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176 }
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177
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178 # read with default values, when applicable
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179 mean_percentile <- args$meanPercentile
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180 sd_percentile <- args$sdPercentile
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181 # in the case of 'random" these values are ignored by the client script
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182 if (imputation_method == "random") {
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183 print("mean_percentile is:")
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184 cat(str(mean_percentile))
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185
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186 print("sd_percentile is:")
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187 cat(str(mean_percentile))
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188 }
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189
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190 # convert string parameters that are passed in via config files:
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191 # - firstDataColumn
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192 # - regexSampleNames
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193 # - regexSampleGrouping
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194 read_config_file_string <- function(fname, limit) {
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195 # eliminate any leading whitespace
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196 result <- gsub("^[ \t\n]*", "", readChar(fname, limit))
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197 # eliminate any trailing whitespace
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198 result <- gsub("[ \t\n]*$", "", result)
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199 # substitute characters escaped by Galaxy sanitizer
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200 result <- gsub("__lt__", "<", result)
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201 result <- gsub("__le__", "<=", result)
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202 result <- gsub("__eq__", "==", result)
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203 result <- gsub("__ne__", "!=", result)
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204 result <- gsub("__gt__", ">", result)
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205 result <- gsub("__ge__", ">=", result)
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206 result <- gsub("__sq__", "'", result)
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207 result <- gsub("__dq__", '"', result)
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208 result <- gsub("__ob__", "[", result)
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209 result <- gsub("__cb__", "]", result)
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210 }
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211 cat(paste0("first_data_column file: ", args$firstDataColumn, "\n"))
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212 cat(paste0("regex_sample_names file: ", args$regexSampleNames, "\n"))
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213 cat(paste0("regex_sample_grouping file: ", args$regexSampleGrouping, "\n"))
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214 nc <- 1000
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215 regex_sample_names <- read_config_file_string(args$regexSampleNames, nc)
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216 regex_sample_grouping <- read_config_file_string(args$regexSampleGrouping, nc)
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217 first_data_column <- read_config_file_string(args$firstDataColumn, nc)
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218 cat(paste0("first_data_column: ", first_data_column, "\n"))
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219 cat(paste0("regex_sample_names: ", regex_sample_names, "\n"))
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220 cat(paste0("regex_sample_grouping: ", regex_sample_grouping, "\n"))
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221
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222 # from: https://github.com/molgenis/molgenis-pipelines/wiki/
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223 # How-to-source-another_file.R-from-within-your-R-script
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224 # Function location_of_this_script returns the location of this .R script
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225 # (may be needed to source other files in same dir)
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226 location_of_this_script <- function() {
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227 this_file <- NULL
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228 # This file may be 'sourced'
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229 for (i in - (1:sys.nframe())) {
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230 if (identical(sys.function(i), base::source)) {
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231 this_file <- (normalizePath(sys.frame(i)$ofile))
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232 }
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233 }
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234
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235 if (!is.null(this_file)) return(dirname(this_file))
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236
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237 # But it may also be called from the command line
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238 cmd_args <- commandArgs(trailingOnly = FALSE)
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239 cmd_args_trailing <- commandArgs(trailingOnly = TRUE)
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240 cmd_args <- cmd_args[
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241 seq.int(
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242 from = 1,
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243 length.out = length(cmd_args) - length(cmd_args_trailing)
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244 )
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245 ]
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246 res <- gsub("^(?:--file=(.*)|.*)$", "\\1", cmd_args)
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247
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248 # If multiple --file arguments are given, R uses the last one
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249 res <- tail(res[res != ""], 1)
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250 if (0 < length(res)) return(dirname(res))
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251
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252 # Both are not the case. Maybe we are in an R GUI?
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253 return(NULL)
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254 }
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255
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256 script_dir <- location_of_this_script()
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257
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258 rmarkdown_params <- list(
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259 inputFile = input_file
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260 , alphaFile = alpha_file
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261 , preprocDb = preproc_sqlite
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262 , firstDataColumn = first_data_column
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263 , imputationMethod = imputation_method
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264 , meanPercentile = mean_percentile
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265 , sdPercentile = sd_percentile
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266 , regexSampleNames = regex_sample_names
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267 , regexSampleGrouping = regex_sample_grouping
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268 , imputedDataFilename = imputed_data_file_name
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269 , imputedQNLTDataFile = imp_qn_lt_data_filenm
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270 , anovaKseaMetadata = anova_ksea_metadata
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271 , kseaAppPrepDb = ksea_sqlite
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272 , kseaCutoffThreshold = ksea_cutoff_threshold
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273 , kseaCutoffStatistic = ksea_cutoff_statistic
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274 )
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275
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276 print("rmarkdown_params")
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277 str(rmarkdown_params)
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278
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279 # freeze the random number generator so the same results will be produced
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280 # from run to run
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281 set.seed(28571)
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282
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283 # BUG (or "opportunity")
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284 # To render as PDF for the time being requires installing the conda
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285 # package `r-texlive` until this issue in `texlive-core` is resolved:
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286 # https://github.com/conda-forge/texlive-core-feedstock/issues/19
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287 # This workaround is detailed in the fourth comment of:
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288 # https://github.com/conda-forge/texlive-core-feedstock/issues/61
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289
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290 library(tinytex)
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291 tinytex::install_tinytex()
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292 rmarkdown::render(
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293 input = paste(script_dir, "mqppep_anova_script.Rmd", sep = "/")
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294 , output_format = rmarkdown::pdf_document(toc = TRUE)
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295 , output_file = report_file_name
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296 , params = rmarkdown_params
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297 )