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annotate masigpro.R @ 0:c8c290f3ea7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
author iuc
date Mon, 15 May 2017 07:29:03 -0400
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children cc96abdef027
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c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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1 #!/usr/bin/env Rscript
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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3 # A command-line interface to maSigPro for use with Galaxy
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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4 # written by Clemens Blank.
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5 # Thanks to Bjoern Gruening and Michael Love for their DESeq2
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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6 # wrapper as a basis to build upon.
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8 # setup R error handling to go to stderr
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9 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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11 # we need that to not crash galaxy with an UTF8 error on German LC settings.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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12 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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14 suppressPackageStartupMessages({
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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15 library("maSigPro")
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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16 library("optparse")
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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17 library("mclust")
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18 })
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20 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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21 args <- commandArgs(trailingOnly = TRUE)
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23 # specify our desired options in a list
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24 # by default OptionParser will add an help option equivalent to
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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25 # make_option(c("-h", "--help"), action="store_true", default=FALSE,
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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26 # help="Show this help message and exit")
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27 option_list <- list(
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28 make_option(c("-q", "--quiet"), action="store_false",
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29 dest="verbose", help="Print little output"),
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30 make_option(c("-e", "--edesign"), type="character"),
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31 make_option(c("-d", "--data"), type="character"),
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32 make_option(c("-o", "--outfile"), type="character"),
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33 make_option("--degree", type="integer", default=1),
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34 make_option("--time_col", type="integer", default=1),
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35 make_option("--repl_col", type="integer", default=2),
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36 make_option("--qvalue", type="double", default=0.05),
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37 make_option("--min_obs", type="integer", default=6),
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38 make_option("--step_method", type="character", default="backward"),
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39 make_option("--nvar_correction", type="logical", default=FALSE),
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40 make_option("--alfa", type="double", default=0.05),
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41 make_option("--rsq", type="double", default=0.7),
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42 make_option("--vars", type="character", default="groups"),
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43 make_option("--significant_intercept", type="character", default="dummy"),
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44 make_option("--cluster_data", type="integer", default=1),
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45 make_option(c("-k", "--k"), type="integer", default=9),
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46 make_option("--cluster_method", type="character", default="hclust"),
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47 make_option("--distance", type="character", default="cor"),
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48 make_option("--agglo_method", type="character", default="ward.D"),
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49 make_option("--iter_max", type="integer", default=500),
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50 make_option("--color_mode", type="character", default="rainbow"),
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51 make_option("--show_fit", type="logical", default=TRUE),
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52 make_option("--show_lines", type="logical", default=TRUE),
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53 make_option("--cexlab", type="double", default=0.8),
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54 make_option("--legend", type="logical", default=TRUE)
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55 )
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56
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57 # get command line options, if help option encountered print help and exit,
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58 # otherwise if options not found on command line then set defaults
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59 opt <- parse_args(OptionParser(option_list=option_list))
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60
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61 # enforce the following required arguments
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62 if (is.null(opt$edesign)) {
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63 cat("'edesign' is required\n")
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64 q(status=1)
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65 }
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66 if (is.null(opt$data)) {
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67 cat("'data' is required\n")
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68 q(status=1)
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69 }
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70 if (is.null(opt$outfile)) {
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71 cat("'outfile' is required\n")
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72 q(status=1)
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73 }
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74
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75 verbose <- if (is.null(opt$quiet)) {
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76 TRUE
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77 } else {
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78 FALSE
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79 }
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80
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81 edesign <- as.matrix(read.table(opt$edesign, header=TRUE, row.names = 1))
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82
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83 data <- read.table(opt$data, header=TRUE)
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84
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85 results <- maSigPro(data, edesign, degree = opt$degree, time.col = opt$time_col,
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86 repl.col = opt$repl_col, Q = opt$qvalue, min.obs = opt$min_obs,
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87 step.method = opt$step_method, nvar.correction = opt$nvar_correction,
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88 alfa = opt$alfa, rsq = opt$rsq, vars = opt$vars,
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89 significant.intercept = opt$significant_intercept,
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90 cluster.data = opt$cluster_data, k = opt$k,
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91 cluster.method = opt$cluster_method, distance = opt$distance,
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92 agglo.method = opt$agglo_method, iter.max = opt$iter_max,
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93 color.mode = opt$color_mode, show.fit = opt$show_fit,
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94 show.lines = opt$show_lines, cexlab = opt$cexlab,
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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95 legend = opt$legend)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
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96
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97 filename <- opt$outfile
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98
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99 write.table((results$summary), file=filename, sep="\t", quote=FALSE,
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100 row.names=FALSE, col.names=TRUE)
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101
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102 cat("Session information:\n\n")
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103
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104 sessionInfo()