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1 ###############################################################################
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2 # In summary this script calculates the z prime factor for one or more plates
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3 # of data.
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4 #
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5 # Args:
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6 # input.data.frame contains one or more columns of plate data. The first column
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7 # must contain the well annotation ie A01, A02 etc. Each subsequent column represents
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8 # a plate of data where the column name is the plate name.
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9 #
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10 # plate.conf.data.frame is a file of the following format:
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11 # well, type(syntax must be either "poscontr" or "negcontr"), name (name of control)
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12 #
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13 # Returns:
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14 # z'factor for each plate for each combination of each type of positive vs negative control.
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15 #
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16 # Author: gouldkate
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17 ###############################################################################
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18
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19 use strict;
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20 use warnings;
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21 use IO::Handle;
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22 use File::Temp qw/ tempfile tempdir /;
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23 my $tdir = tempdir( CLEANUP => 0 );
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24
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25 # check to make sure having correct input and output files
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26 my $usage = "usage: calculateZPrimeFactor.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
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27 die $usage unless @ARGV == 3;
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28
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29 #get the input arguments
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30 my $plateData = $ARGV[0];
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31 my $plateConfig = $ARGV[1];
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32 my $zPrimeFactor = $ARGV[2];
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33
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34 #open the input files
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35 open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n");
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36 open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n");
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37 open (OUTPUT1, ">", $zPrimeFactor) || die("Could not open file $zPrimeFactor \n");
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38
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39 #variable to store the name of the R script file
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40 my $r_script;
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41
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42 # R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values
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43 # construct an R script file and save it in a temp directory
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44 chdir $tdir;
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45 $r_script = "calculateZPrimeFactor.r";
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46
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47 open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
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48 print Rcmd "
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49 #options(show.error.messages = FALSE);
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50 input.data.frame <- read.table(\"$plateData\", head=T, sep=\"\\t\", comment=\"\");
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51 plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\");
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52
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53 # assumed second column is type ie negcontr or poscontr and third column is name of control
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54 negative.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"negcontr\"),][,3])
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55 positive.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"poscontr\"),][,3])
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56
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57 z.prime.factor.report.data.frame <- data.frame()
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58
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59
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60 for (negative.control in negative.controls.list){
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61 for (positive.control in positive.controls.list){
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62 for (i in 2:length(colnames(input.data.frame))){
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63
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64 negative.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == negative.control),][,1]
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65 positive.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == positive.control),][,1]
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66
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67 control.duo <- paste(negative.control, positive.control, sep=\"/\")
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68
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69 negative.control.values <- input.data.frame[((input.data.frame[,1] %in% negative.control.wells)&(!(is.na(input.data.frame[,i])))),][,i]
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70 positive.control.values <- input.data.frame[((input.data.frame[,1] %in% positive.control.wells)&(!(is.na(input.data.frame[,i])))),][,i]
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71
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72 if ((length(negative.control.values)==0)|(length(positive.control.values)==0)){
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73 z.prime.factor <- NA
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74 } else {
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75 if ((sum(negative.control.values)) < (sum(positive.control.values))){
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76 low.value.controls <- negative.control.values
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77 high.value.controls <- positive.control.values
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78 } else {
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79 low.value.controls <- positive.control.values
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80 high.value.controls <- negative.control.values
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81 }
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82 z.prime.factor <- round(1 - ((3 * (sd(high.value.controls, na.rm = TRUE) + sd(low.value.controls, na.rm = TRUE))/(abs(mean(high.value.controls, na.rm = TRUE) - mean(low.value.controls, na.rm = TRUE))))), 2)
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83 }
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84
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85 plate.name <- colnames(input.data.frame)[i]
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86 z.prime.factor.current.row.data.frame <- data.frame(plate=plate.name, control.duo=control.duo, z.prime.factor=z.prime.factor, stringsAsFactors=FALSE)
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87 z.prime.factor.report.data.frame <-rbind(z.prime.factor.report.data.frame, z.prime.factor.current.row.data.frame)
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88 }
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89 }
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90 }
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91 z.prime.factor.report.data.frame <- z.prime.factor.report.data.frame[order(z.prime.factor.report.data.frame\$control.duo),]
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92 write.table(z.prime.factor.report.data.frame, file=\"$zPrimeFactor\", quote=F, sep=\"\\t\", row.names=F);
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93 #eof\n";
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94
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95 close Rcmd;
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96
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97 system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
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98
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99 #close the input and output files
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100 close(OUTPUT1);
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101 close(INPUT1);
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102 close(INPUT2);
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