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robustZScoreNormalization.pl robustZScoreNormalization.xml test-data/150615-HR-12015-01A.linear test-data/calc_robust_z.tabular test-data/plate_config.txt |
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| diff -r 000000000000 -r 7ecbc3ec2f55 robustZScoreNormalization.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/robustZScoreNormalization.pl Wed Jun 01 03:59:51 2016 -0400 |
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| @@ -0,0 +1,76 @@ +############################################################################### +# In summary this script calculates the robust z score for one or more plates +# of data. +# +# Args: +# input.data.frame contains one or more columns of plate data. The first column +# must contain the well annotation ie A01, A02 etc. Each subsequent column represents +# a plate of data where the column name is the plate name. +# +# plate.conf.data.frame is a file of the following format: +# well, type (syntax must be either "poscontr" or "negcontr" or "empty"), name (name of control) +# +# Returns: +# robust z score normalized values per plate. +# +# Author: kate gould +############################################################################### + +use strict; +use warnings; +use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); + +# check to make sure having correct input and output files +my $usage = "usage: robustZScoreNormalization.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n"; +die $usage unless @ARGV == 3; + +#get the input arguments +my $plateData = $ARGV[0]; +my $plateConfig = $ARGV[1]; +my $zNorm = $ARGV[2]; + +#open the input files +open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n"); +open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n"); +open (OUTPUT1, ">", $zNorm) || die("Could not open file $zNorm \n"); + +#variable to store the name of the R script file +my $r_script; + +# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values +# construct an R script file and save it in a temp directory +chdir $tdir; +$r_script = "robustZScoreNormalization.r"; + +open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; +print Rcmd " + #options(show.error.messages = FALSE); + header <- read.table(\"$plateData\", head=F, sep=\"\\t\", comment=\"\", nrows=1); + input.data.frame <- read.table(\"$plateData\", head=F, sep=\"\\t\", skip=1); + plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\"); + + # assumed second column is type ie negcontr or poscontr and third column is name of control + excluded.wells <- unique(plate.conf.data.frame[,1]) + + robust.z.score.normalise <- function(x, y) return ((x-median(y))/mad(y)) + robust.z.score.normalisation.data.frame <- data.frame(well=input.data.frame[,1], stringsAsFactors=FALSE) + + for (i in 2:length(colnames(input.data.frame))){ + replicate.sample.values <- input.data.frame[((!(input.data.frame[,1] %in% excluded.wells))&(!(is.na(input.data.frame[,i])))),][,i] + robust.z.score.normalisation.data.frame <- cbind(robust.z.score.normalisation.data.frame, round(sapply(input.data.frame[,i], FUN=robust.z.score.normalise, replicate.sample.values), 2)) + } + names(robust.z.score.normalisation.data.frame) <- names(input.data.frame) + write.table(header, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F); + write.table(robust.z.score.normalisation.data.frame, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F, append=T); + #eof\n"; + +close Rcmd; + +system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); + +#close the input and output files +close(OUTPUT1); +close(INPUT1); +close(INPUT2); |
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| diff -r 000000000000 -r 7ecbc3ec2f55 robustZScoreNormalization.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/robustZScoreNormalization.xml Wed Jun 01 03:59:51 2016 -0400 |
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| @@ -0,0 +1,137 @@ +<tool id="robustZScoreNormalization" name="Calculate Robust Z Score Normalization" version="1.0.0"> + <description>Per Plate</description> + + <command interpreter="perl"> + robustZScoreNormalization.pl $inputFile1 $inputFile2 $outputFile1 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/> + <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/> + </inputs> + + <outputs> + <data format="tabular" name="outputFile1"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="150615-HR-12015-01A.linear"/> + <param name="inputFile2" value="plate_config.txt"/> + <output name="outputFile1" file="calc_robust_z.tabular"/> + </test> + </tests> + + + <help> + +.. class:: infomark + +**What it does** + +This program takes a linear plate table and a plate config file as input and then performs Robust Z Score Normalization on the data. +The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**. + +**Example** + +If the plates table consisted of:: + + #Well Table_1 Table_2 A01 1654 6 A02 1719 8 A03 1624 19 A04 1518 6 A05 1587 12 A06 1517 8 A07 1638 9 A08 1733 7 A09 1617 6 A10 1722 8 ... + P14 1630 6 P15 1576 6 P16 1740 7 P17 1578 6 P18 1544 6 P19 1692 6 P20 1560 6 P21 1552 6 P22 1790 7 P23 1537 6 P24 NA NA + +and the plates config was:: + + #Well Type Name A02 negcontr NT2 + B02 negcontr NT2 + C02 poscontr ASCIZ + D02 poscontr PARP + E02 negcontr NT2 + F02 poscontr ASCIZ + G02 poscontr PARP + H02 negcontr NT2 + I02 poscontr ASCIZ + J02 poscontr PARP + K02 negcontr NT2 + L02 poscontr ASCIZ + M02 poscontr PARP + N02 negcontr NT2 + O02 poscontr ASCIZ + P02 negcontr NT2 + A23 negcontr NT2 + B23 negcontr NT2 + C23 poscontr ASCIZ + D23 poscontr PARP + E23 negcontr NT2 + F23 poscontr ASCIZ + G23 poscontr PARP + H23 negcontr NT2 + I23 poscontr ASCIZ + J23 poscontr PARP + K23 negcontr NT2 + L23 poscontr ASCIZ + M23 poscontr PARP + N23 negcontr NT2 + O23 poscontr ASCIZ + P23 negcontr NT2 + A01 exclude exclude + A24 exclude exclude + B01 exclude exclude + B24 exclude exclude + C01 exclude exclude + C24 exclude exclude + D01 exclude exclude + D24 exclude exclude + E01 exclude exclude + E24 exclude exclude + F01 exclude exclude + F24 exclude exclude + G01 exclude exclude + G24 exclude exclude + H01 exclude exclude + H24 exclude exclude + I01 exclude exclude + I24 exclude exclude + J01 exclude exclude + J24 exclude exclude + K01 exclude exclude + K24 exclude exclude + L01 exclude exclude + L24 exclude exclude + M01 exclude exclude + M24 exclude exclude + N01 exclude exclude + N24 exclude exclude + O01 exclude exclude + O24 exclude exclude + P01 exclude exclude + P24 exclude exclude + +Running the program will give the following output:: + + #Well Table_1 Table_2 + A01 0.74 -0.67 + A02 1.55 0.67 + A03 0.36 8.09 + A04 -0.96 -0.67 + A05 -0.1 3.37 + A06 -0.97 0.67 + A07 0.54 1.35 + A08 1.72 0 + A09 0.27 -0.67 + A10 1.59 0.67 + ... + P14 0.44 -0.67 + P15 -0.24 -0.67 + P16 1.81 0 + P17 -0.21 -0.67 + P18 -0.64 -0.67 + P19 1.21 -0.67 + P20 -0.44 -0.67 + P21 -0.54 -0.67 + P22 2.44 0 + P23 -0.72 -0.67 + P24 NA NA + + </help> + +</tool> |
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| diff -r 000000000000 -r 7ecbc3ec2f55 test-data/150615-HR-12015-01A.linear --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/150615-HR-12015-01A.linear Wed Jun 01 03:59:51 2016 -0400 |
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| b'@@ -0,0 +1,385 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|
| b |
| diff -r 000000000000 -r 7ecbc3ec2f55 test-data/calc_robust_z.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/calc_robust_z.tabular Wed Jun 01 03:59:51 2016 -0400 |
| b |
| b'@@ -0,0 +1,385 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|
| b |
| diff -r 000000000000 -r 7ecbc3ec2f55 test-data/plate_config.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plate_config.txt Wed Jun 01 03:59:51 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +well type name geneID B02 poscontr Hamp 57817 C02 negcontr OTP -1 D02 poscontr PLK 5347 E02 poscontr TOX -1 F02 negcontr OTP -1 G02 poscontr MPEG1 17476 H02 poscontr TOX -1 I02 poscontr PLK 5347 J02 negcontr OTP -1 K02 poscontr TOX -1 L02 poscontr Hamp 57817 M02 negcontr OTP -1 N02 poscontr PLK 5347 O02 negcontr mock -1 B23 poscontr PLK 5347 C23 negcontr OTP -1 D23 poscontr TOX -1 E23 negcontr OTP -1 F23 poscontr PLK 5347 G23 poscontr MPEG1 17476 H23 poscontr TOX -1 I23 negcontr OTP -1 J23 poscontr PLK 5347 K23 poscontr Hamp 57817 L23 negcontr OTP -1 M23 poscontr MPEG1 17476 N23 negcontr OTP -1 O23 negcontr mock -1 \ No newline at end of file |