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1 #!/usr/bin/env Rscript
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2
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3 # Compute metrics (all except PCA) for ROI files.
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4 #
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5 # USAGE: roi_metrics.Rscript -i IN.roi -o OUT.roi
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6
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7 # TODO(holtgrew): Bernd, can you give the English names of the metrics below in the comments?
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8
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9 # Author: Bernd Jagla <bernd.jagla@pasteur.fr>
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10 # Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
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11
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12 library('getopt') # parsing args
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13 library('ngsroi') # ROI I/O
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14 library('boot') # k3.linear()
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15
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16 # ----------------------------------------------------------------------------
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17 # Command Line Parsing
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18 # ----------------------------------------------------------------------------
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19
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20 # Parse command line options.
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21 spec = matrix(c(
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22 "help", "h", 0, "logical",
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23 "infile", "i", 1, "character",
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24 "outfile", "o", 1, "character"
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25 ), byrow=TRUE, ncol=4);
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26 opt = getopt(spec);
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27
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28 # If help was asked for print a friendly message and exit with a non-zero
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29 # error code.
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30 if (!is.null(opt$help) )
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31 {
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32 cat(getopt(spec, usage=TRUE));
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33 q(status=1);
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34 }
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35
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36 # Check arguments.
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37 if (is.null(opt$infile))
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38 {
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39 write("-i/--infile missing.", stderr());
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40 q(status=1)
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41 }
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42 if (is.null(opt$out))
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43 {
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44 write("-o/--outfile missing.", stderr());
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45 q(status=1)
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46 }
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47
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48 # ----------------------------------------------------------------------------
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49 # Compute metrics.
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50 # ----------------------------------------------------------------------------
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51
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1
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52 # Read input files.
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0
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53 roi = readROI(opt$infile)
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54
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55 # Compute some basic statistics.
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56 roi$min = as.numeric(lapply(roi$counts, min))
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57 roi$median = as.numeric(lapply(roi$counts, median))
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58 roi$mean = as.numeric(lapply(roi$counts, mean))
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59 roi$quantile75 = as.numeric(lapply(roi$counts, quantile, probs=0.75))
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60 roi$quantile95 = as.numeric(lapply(roi$counts, quantile, probs=0.95))
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61
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62 # Compute area under curve metric.
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63 aoc <- function(v){
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64 m = max(v)
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65 return (sum(v/m)/length(v))
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66 }
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67 roi$aoc = as.numeric(lapply(roi$counts, aoc))
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68
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69 # Compute xreaXX metric.
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70 xreaXX <- function(v){
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71 vo=order(v)
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72 mx = max(v)
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73 mi = min(v)
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74 if((mx-mi)==0) return(0)
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75 vn=(v-mi)/(mx-mi)
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76 x=c(1:length(v))/length(v)
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77 vno=vn[vo]
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78 return(sum(x-vno)/length(v))
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79 }
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80 roi$xreaXX = as.numeric(lapply(roi$counts, xreaXX))
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81
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82 # Compute r3linear metric.
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83 roi$r3linear = as.numeric(lapply(roi$counts, k3.linear))
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84
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85 # Compute distMax3p metric.
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86 distMax3p <- function(v)
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87 {
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88 return(length(v)-which.max(rev(v))+1)
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89 }
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90 roi$distMax3p = as.numeric(lapply(roi$count, distMax3p))
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91
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92 # Compute distMax5p metric.
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93 distMax5p <- function(v)
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94 {
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95 return (which.max(v))
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96 }
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97 roi$distMax5p = as.numeric(lapply(roi$count, distMax5p))
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98
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99 # Write output.
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100 writeROI(roi, opt$outfile)
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101
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102 # Quit with success code.
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103 q(status=0) |
