Mercurial > repos > devteam > compute_q_values
changeset 0:63abfc350814
Imported from capsule None
author | devteam |
---|---|
date | Tue, 01 Apr 2014 10:53:54 -0400 |
parents | |
children | 62f7b9c20c9b |
files | compute_q_values.pl compute_q_values.xml test-data/p_q_hists_Q_plots.pdf test-data/p_values.tabular test-data/q_values.tabular tool_dependencies.xml |
diffstat | 6 files changed, 1359 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compute_q_values.pl Tue Apr 01 10:53:54 2014 -0400 @@ -0,0 +1,95 @@ +# A program to compute the q-values based on the p-values of multiple simultaneous tests. +# The q-valules are computed using a specific R package created by John Storey called "qvalue". +# The input is a TABULAR format file consisting of one column only that represents the p-values +# of multiple simultaneous tests, one line for every p-value. +# The first output is a TABULAR format file consisting of one column only that represents the q-values +# corresponding to p-values, one line for every q-value. +# the second output is a TABULAR format file consisting of three pages: the first page represents +# the p-values histogram, the second page represents the q-values histogram, and the third page represents +# the four Q-plots as introduced in the "qvalue" package manual. + +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: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n"; +die $usage unless @ARGV == 7; + +#get the input arguments +my $p_valuesInputFile = $ARGV[0]; +my $lambdaValue = $ARGV[1]; +my $pi0_method = $ARGV[2]; +my $fdr_level = $ARGV[3]; +my $robustValue = $ARGV[4]; +my $q_valuesOutputFile = $ARGV[5]; +my $p_q_values_histograms_QPlotsFile = $ARGV[6]; + +if($lambdaValue =~ /sequence/){ + $lambdaValue = "seq(0, 0.95, 0.05)"; +} + +#open the input files +open (INPUT, "<", $p_valuesInputFile) || die("Could not open file $p_valuesInputFile \n"); +open (OUTPUT1, ">", $q_valuesOutputFile) || die("Could not open file $q_valuesOutputFile \n"); +open (OUTPUT2, ">", $p_q_values_histograms_QPlotsFile) || die("Could not open file $p_q_values_histograms_QPlotsFile \n"); +#open (ERROR, ">", "error.txt") or die ("Could not open file error.txt \n"); + +#save all error messages into the error file $errorFile using the error file handle ERROR +#STDERR -> fdopen( \*ERROR, "w" ) or die ("Could not direct errors to the error file error.txt \n"); + +#warn "Hello Error File \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 = "q_values_computation.r"; + +open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; +print Rcmd " + #options(show.error.messages = FALSE); + + #load necessary packages + suppressPackageStartupMessages(library(tcltk)); + library(qvalue); + + #read the p-values of the multiple simultaneous tests from the input file $p_valuesInputFile + p <- scan(\"$p_valuesInputFile\", quiet = TRUE); + + #compute the q-values that correspond to the p-values of the multiple simultaneous tests + qobj <- qvalue(p, pi0.meth = \"$pi0_method\", lambda = $lambdaValue, fdr.level = $fdr_level, robust = $robustValue); + #qobj <- qvalue(p, pi0.meth = \"smoother\", lambda = seq(0, 0.95, 0.05), fdr.level = 0.05); + #qobj <- qvalue(p, pi0.meth = \"bootstrap\", fdr.level = 0.05); + + #draw the p-values histogram, the q-values histogram, and the four Q-plots + # and save them on multiple pages of the output file $p_q_values_histograms_QPlotsFile + pdf(file = \"$p_q_values_histograms_QPlotsFile\", width = 6.25, height = 6, family = \"Times\", pointsize = 12, onefile = TRUE) + hist(qobj\$pvalues); + #dev.off(); + + hist(qobj\$qvalues); + #dev.off(); + + qplot(qobj); + dev.off(); + + #save the q-values in the output file $q_valuesOutputFile + qobj\$pi0 <- signif(qobj\$pi0,digits=6) + qwrite(qobj, filename=\"$q_valuesOutputFile\"); + + #options(show.error.messages = TRUE); + #eof\n"; +close Rcmd; + +system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); + +#close the input and output and error files +#close(ERROR); +close(OUTPUT2); +close(OUTPUT1); +close(INPUT);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compute_q_values.xml Tue Apr 01 10:53:54 2014 -0400 @@ -0,0 +1,158 @@ +<tool id="compute_q_values" name="Compute q-values" version="1.0.1"> + <description>based on multiple simultaneous tests p-values</description> + <requirements> + <requirement type="package" version="2.11.0">R</requirement> + <requirement type="package" version="1.34.0">bioc_qvalue</requirement> + </requirements> + <command interpreter="perl"> + compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select the p-values file"/> + + <param type="text" name="inputLambda2" size="100" value="sequence_from_0_to_0.95_increment_0.05" label="What is the lambda value?" help="Either choose the default sequence or one deciaml value between 0 and 1"/> + + <param name="inputPI0_method3" type="select" label="Choose the PI method:"> + <option value="smoother">smoother</option> + <option value="bootstrap">bootstrap</option> + </param> + + <param type="float" name="inputFDR_level4" size="5" value="" label="What is the FDR level?" help="The FDR level must be between 0 and 1"/> + + <param name="inputRobust5" type="select" label="Do you want to make the estimate more robust:" help="Choose TRUE for small p-values"> + <option value="FALSE">FALSE</option> + <option value="TRUE">TRUE</option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="outputFile1"/> + <data format="pdf" name="outputFile2"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="p_values.tabular" ftype="tabular" /> + <param name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" /> + <param name="inputPI0_method3" value="smoother" /> + <param name="inputFDR_level4" value="0.05" /> + <param name="inputRobust5" value="FALSE" /> + <output name="outputFile1" file="q_values.tabular" /> + <output name="outputFile1" file="p_q_hists_Q_plots.pdf" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This program computes the q-values based on the p-values of multiple simultaneous tests. The q-values are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs: + +- The first input is a TABULAR format file consisting of one column only that represents the p-values of multiple simultaneous tests, one line for every p-value. +- The second input is the lambda parameter. The user can choose either the default: seq(0, 0.95, 0.05) or a decimal number between 0.0 and 1.0. +- The third input is PI method which is either "smoother" or "bootstrap". +- The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0. +- The fifth input is either TRUE or FALSE for the estimate robustness. + +The program gives two outputs: + +- The first output is a TABULAR format file consisting of three columns: + + - the left column represents the p-values of multiple simultaneous tests, one line for every p-value + - the middle column represents the q-values corresponding to the p-values + - the third column represent the significance values, either 1 for significant or 0 for non-significant + +- The second output is a PDF format file consisting of three pages: + + - the first page represents the p-values histogram + - the second page represents the q-values histogram + - the third page represents the four Q-plots as introduced in the "qvalue" package manual. + + +**Example** + +Let us have the first input file of p-values as follows:: + + 0.140627492 + 0.432249886 + 0.122120877 + 0.142010182 + 0.012909858 + 0.000142807 + 0.039841941 + 0.035173303 + 0.011340057 + 1.01E-05 + 0.212738282 + 0.091256284 + 0.547375415 + 0.189589833 + 6.18E-12 + 0.001235875 + 1.10E-05 + 9.75E-07 + 2.13E-18 + 2.54E-16 + 1.20E-19 + 9.76E-14 + 0.359181534 + 0.03661672 + 0.400459987 + 0.387436466 + 0.342075061 + 0.904129283 + 0.031152635 + +Running the program will give the following output:: + + pi0: 0.140311054 + + FDR level: 0.05 + + p-value q-value significant + 0.1406275 0.02889212 1 + 0.4322499 0.06514199 0 + 0.1221209 0.02760624 1 + 0.1420102 0.02889212 1 + 0.01290986 0.00437754 1 + 0.000142807 6.46E-05 1 + 0.03984194 0.01013235 1 + 0.0351733 0.009932946 1 + 0.01134006 0.004194811 1 + 1.01E-05 5.59E-06 1 + 0.2127383 0.03934711 1 + 0.09125628 0.02184257 1 + 0.5473754 0.07954578 0 + 0.1895898 0.03673547 1 + 6.18E-12 5.03E-12 1 + 0.001235875 0.00050288 1 + 1.10E-05 5.59E-06 1 + 9.75E-07 6.61E-07 1 + 2.13E-18 4.33E-18 1 + 2.54E-16 3.45E-16 1 + 1.20E-19 4.88E-19 1 + 9.76E-14 9.93E-14 1 + 0.3591815 0.06089654 0 + 0.03661672 0.009932946 1 + 0.40046 0.0626723 0 + 0.3874365 0.0626723 0 + 0.3420751 0.06051785 0 + 0.9041293 0.1268593 0 + 0.03115264 0.009750824 1 + + +.. image:: ${static_path}/operation_icons/p_hist.png + + +.. image:: ${static_path}/operation_icons/q_hist.png + + +.. image:: ${static_path}/operation_icons/Q_plots.png + + + </help> + +</tool>
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l S +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 259.66 272.13 Tm (0.00) Tj +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 259.66 311.98 Tm (0.04) Tj +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 259.66 351.82 Tm (0.08) Tj +ET +274.00 276.96 m +424.90 276.96 l +424.90 383.00 l +274.00 383.00 l +274.00 276.96 l +S +Q q 225.00 216.00 225.00 216.00 re W n +BT +0.000 0.000 0.000 rg +/F2 1 Tf 10.00 0.00 -0.00 10.00 333.43 231.54 Tm [(p-v) 25 (alue)] TJ +ET +BT +/F2 1 Tf 0.00 10.00 -10.00 0.00 235.76 313.95 Tm [(q-v) 25 (alue)] TJ +ET +Q q 49.00 60.96 150.90 106.04 re W n +Q q 49.00 60.96 150.90 106.04 re W n +0.000 0.000 0.000 RG +0.75 w +[] 0 d +1 J +1 j +10.00 M +54.59 64.88 m +54.59 66.49 l +54.59 68.10 l +54.59 69.71 l +54.59 71.32 l +54.59 72.93 l +54.59 74.54 l +54.59 76.15 l +54.59 77.76 l +54.59 79.37 l +54.59 80.98 l +54.59 82.59 l +54.59 84.20 l +54.59 85.81 l +54.59 87.42 l +54.59 89.03 l +54.59 90.64 l +54.59 92.25 l +54.61 93.86 l +54.61 95.47 l +54.61 97.08 l +54.80 98.68 l +54.82 100.29 l 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/p_values.tabular Tue Apr 01 10:53:54 2014 -0400 @@ -0,0 +1,104 @@ +0.140627492 +0.432249886 +0.122120877 +0.142010182 +0.012909858 +0.000142807 +0.039841941 +0.035173303 +0.011340057 +1.01E-05 +0.212738282 +0.091256284 +0.547375415 +0.189589833 +6.18E-12 +0.001235875 +1.10E-05 +9.75E-07 +2.13E-18 +2.54E-16 +1.20E-19 +9.76E-14 +0.359181534 +0.03661672 +0.400459987 +0.387436466 +0.342075061 +0.904129283 +0.031152635 +0.192291058 +0.437124583 +0.277275459 +0.087793283 +0.212338628 +0.240978806 +0.147992575 +0.29686964 +1.76E-25 +0.000177302 +0.723415697 +0.082881604 +0.406304527 +0.281528123 +0.83848178 +0.622982165 +0.384561646 +0.386866855 +0.117564737 +0.001311515 +0.025337876 +0.317341701 +0.758855602 +0.893904741 +0.192291058 +0.534845889 +0.119743614 +0.122225863 +0.00321982 +0.393640803 +0.851268223 +0.206016554 +0.493358194 +0.221548695 +0.050657449 +0.650946275 +0.000766626 +0.017573735 +1.04E-05 +0.000129641 +0.000160473 +1.66E-10 +1.98E-16 +5.14E-08 +0.212786809 +0.003709354 +0.379936041 +0.293121715 +1.80E-27 +1.38E-20 +9.55E-07 +3.40E-37 +0.569660945 +0.277275459 +0.083264512 +0.993910216 +0.929394391 +0.277275459 +0.445814529 +0.034816588 +0.259597445 +0.425425014 +0.45953669 +0.443668416 +0.317341701 +1.35E-08 +1.51E-12 +1.21E-07 +7.58E-12 +0.124718201 +0.747944686 +0.413176878 +0.157312584 +0.828166803 +0.295507577
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/q_values.tabular Tue Apr 01 10:53:54 2014 -0400 @@ -0,0 +1,109 @@ +pi0: 0.243864 + +FDR level: 0.05 + +p-value q-value significant +0.1406275 0.07062033 0 +0.4322499 0.1299617 0 +0.1221209 0.06455266 0 +0.1420102 0.07062033 0 +0.01290986 0.01023180 1 +0.000142807 0.0001574715 1 +0.03984194 0.02590934 1 +0.0351733 0.0241097 1 +0.01134006 0.009277564 1 +1.01e-05 1.318815e-05 1 +0.2127383 0.08994434 0 +0.09125628 0.05260058 0 +0.5473754 0.1525542 0 +0.1895898 0.08708663 0 +6.18e-12 1.424873e-11 1 +0.001235875 0.001160890 1 +1.1e-05 1.328476e-05 1 +9.75e-07 1.373765e-06 1 +2.13e-18 9.003446e-18 1 +2.54e-16 8.052378e-16 1 +1.2e-19 6.086837e-19 1 +9.76e-14 2.750348e-13 1 +0.3591815 0.1231013 0 +0.03661672 0.02443860 1 +0.40046 0.1269549 0 +0.3874365 0.1259756 0 +0.3420751 0.1188445 0 +0.9041293 0.2248075 0 +0.03115264 0.02257393 1 +0.1922911 0.08708663 0 +0.4371246 0.1299617 0 +0.2772755 0.1065486 0 +0.08779328 0.05178133 0 +0.2123386 0.08994434 0 +0.2409788 0.09857518 0 +0.1479926 0.07218002 0 +0.2968696 0.1075593 0 +1.76e-25 1.487893e-24 1 +0.000177302 0.0001798681 1 +0.7234157 0.1931278 0 +0.0828816 0.05027951 0 +0.4063045 0.1272176 0 +0.2815281 0.1065681 0 +0.8384818 0.2148023 0 +0.6229822 0.1698921 0 +0.3845616 0.1259756 0 +0.3868669 0.1259756 0 +0.1175647 0.06455266 0 +0.001311515 0.001187943 1 +0.02533788 0.01890043 1 +0.3173417 0.1117828 0 +0.7588556 0.1984119 0 +0.8939047 0.2244658 0 +0.1922911 0.08708663 0 +0.5348459 0.1507185 0 +0.1197436 0.06455266 0 +0.1222259 0.06455266 0 +0.00321982 0.002815879 1 +0.3936408 0.1263727 0 +0.8512682 0.2158971 0 +0.2060166 0.08994434 0 +0.4933582 0.1405895 0 +0.2215487 0.09211275 0 +0.05065745 0.03211913 1 +0.6509463 0.1756296 0 +0.000766626 0.0007478089 1 +0.01757374 0.01350612 1 +1.04e-05 1.318815e-05 1 +0.000129641 0.0001494514 1 +0.000160473 0.0001695786 1 +1.66e-10 3.238509e-10 1 +1.98e-16 7.173772e-16 1 +5.14e-08 8.69065e-08 1 +0.2127868 0.08994434 0 +0.003709354 0.003135866 1 +0.3799360 0.1259756 0 +0.2931217 0.1075593 0 +1.8e-27 2.282564e-26 1 +1.38e-20 8.749828e-20 1 +9.55e-07 1.373765e-06 1 +3.4e-37 8.623019e-36 1 +0.569661 0.1570395 0 +0.2772755 0.1065486 0 +0.08326451 0.05027951 0 +0.9939102 0.2423786 0 +0.9293944 0.2288459 0 +0.2772755 0.1065486 0 +0.4458145 0.1299617 0 +0.03481659 0.0241097 1 +0.2595974 0.1045058 0 +0.425425 0.1299617 0 +0.4595367 0.1324396 0 +0.4436684 0.1299617 0 +0.3173417 0.1117828 0 +1.35e-08 2.445604e-08 1 +1.51e-12 3.829635e-12 1 +1.21e-07 1.917988e-07 1 +7.58e-12 1.602022e-11 1 +0.1247182 0.06455266 0 +0.7479447 0.1975962 0 +0.4131769 0.1277917 0 +0.1573126 0.07527799 0 +0.8281668 0.2143247 0 +0.2955076 0.1075593 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 10:53:54 2014 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="2.11.0"> + <repository changeset_revision="6e1b17857732" name="package_r_2_11_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bioc_qvalue" version="1.34.0"> + <repository changeset_revision="11735242a19e" name="package_bioc_qvalue_1_34_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>