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1 #!/usr/bin/Rscript
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2
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3 #-----------------------------------#
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4 # Author: Maude #
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5 # Script: estimateSign_Galaxy.r #
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6 # Last update: 22/07/15 #
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7 #-----------------------------------#
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8
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9 #########################################################################################################################################
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10 # Estimate the number of signatures for NMF #
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11 #########################################################################################################################################
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12
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13 #-------------------------------------------------------------------------------
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14 # Load library for recovering the arguments
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15 #-------------------------------------------------------------------------------
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16 suppressMessages(suppressWarnings(require("getopt")))
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17
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18
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19 #-------------------------------------------------------------------------------
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20 # Recover the arguments
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21 #-------------------------------------------------------------------------------
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22 spec = matrix(c(
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23 "input" , "i", 1, "character",
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24 "stop", "stop", 1, "numeric",
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25 "cpu", "cpu", 1, "integer",
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26 "output", "o", 1, "character",
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27 "help", "h", 0, "logical"
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28 ),
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29 byrow=TRUE, ncol=4
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30 )
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31
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32 opt = getopt(spec);
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33
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34 # No argument is pass to the command line
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35 if(length(opt) == 1)
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36 {
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37 cat(paste("Usage:\n estimateSign_Galaxy.r --input <matrix> --stop <maxNbSign> --cpu <cpu> --output <output_filename.png>\n",sep=""))
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38 q(status=1)
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39 }
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40
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41 # Help was asked for.
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42 if ( !is.null(opt$help) )
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43 {
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44 # print a friendly message and exit with a non-zero error code
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45 cat(paste("Usage:\n estimateSign_Galaxy.r --input <matrix> --stop <maxNbSign> --cpu <cpu> --output <output_filename.png>\n",sep=""))
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46 q(status=1)
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47 }
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48
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49
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50
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51 #-------------------------------------------------------------------------------
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52 # Load library
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53 #-------------------------------------------------------------------------------
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54 suppressMessages(suppressWarnings(library(NMF)))
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55
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56
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57 ###############################################################################
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58 # Load the functions #
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59 ###############################################################################
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60
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61 #-------------------------------------------------------------------------------
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62 # Check the file doesn't have lines equal to zero
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63 #-------------------------------------------------------------------------------
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64 CheckFile <- function(rowsum, dataFrame, x)
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65 {
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66 if(rowsum == 0)
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67 {
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68 write("\n\nERROR: There is not enough mutations for running NMF!!!", stderr())
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69 write(paste0("Input matrix contains at least one null row ", rownames(dataFrame)[x], "\n\n"), stderr())
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70 stop()
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71 }
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72 }
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73
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74
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75 ###############################################################################
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76 # Check file #
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77 ###############################################################################
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78
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79 # The input musn't contains lines equal to zero !!!
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80 matrixNMF <- read.table(opt$input, header=T)
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81 # suppresses the return of sapply function
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82 invisible( sapply(1:nrow(matrixNMF), function(x) { CheckFile(rowSums(matrixNMF)[x], matrixNMF, x) } ) )
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83
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84
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85
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86 ###############################################################################
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87 # Estimate the number of signatures #
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88 ###############################################################################
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89 # Estimate the number of signatures with our data
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90 nbCPU <- paste0("vP", opt$cpu)
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91 nbSign <- 2:opt$stop # The minum number of signatures can't be lower than 2
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92
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93 estim_r <- nmf(matrixNMF, method="brunet", nbSign, nrun=50, .opt=nbCPU)
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94
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95 # Shuffle original data
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96 v_random <- randomize(matrixNMF)
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97 # Estimate quality measures from the shuffled data
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98 estim_r_random <- nmf(v_random, method="brunet", nbSign, nrun=50, .opt=nbCPU)
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99
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100 # Plot the estimation for our data and the random ones
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101 graphics.off()
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102 options(bitmapType='cairo')
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103 png(opt$output, width=3000, height=2000, res=300)
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104 plot(estim_r, estim_r_random)
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105 invisible( dev.off() )
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