| Previous changeset 55:7698612e1dc7 (2017-05-31) Next changeset 57:6e478392eff2 (2017-06-08) |
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Commit message:
Uploaded 20170608 |
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modified:
loadandplot.xml plotwithscale.xml testandplot.xml |
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added:
._loadandplot.R ._plotwithscale.R ._testandplot.R test-data/._.DS_Store test-data/input/._Controls_regions.bed test-data/input/._Elements1_regions.bed test-data/input/._Elements2_regions.bed test-data/input/._Elements3_regions.bed test-data/input/._Feature1.bed test-data/input/._Feature2.bed test-data/input/._features.header.bed.txt test-data/input/._regions.header.txt test-data/input/Controls_regions.bed test-data/input/Elements1_regions.bed test-data/input/Elements2_regions.bed test-data/input/Elements3_regions.bed test-data/input/Feature1.bed test-data/input/Feature2.bed test-data/input/features.header.bed.txt test-data/input/regions.header.txt test-data/output_loadandplot/._iwtomics.loadandplot.RData test-data/output_loadandplot/._iwtomics.loadandplot.features.txt test-data/output_loadandplot/._iwtomics.loadandplot.pdf test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt test-data/output_loadandplot/iwtomics.loadandplot.RData test-data/output_loadandplot/iwtomics.loadandplot.features.txt test-data/output_loadandplot/iwtomics.loadandplot.pdf test-data/output_loadandplot/iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.RData test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.tests.txt test-data/output_testandplot/iwtomics.testandplot.RData test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/iwtomics.testandplot.tests.txt |
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removed:
ETn_example/Control.bed ETn_example/DESCRIPTION.txt ETn_example/ETn_fixed.bed ETn_example/Recombination_hotspots.txt ETn_example/features.header ETn_example/regions.header example/Controls_regions.bed example/DESCRIPTION.txt example/Elements1_regions.bed example/Elements2_regions.bed example/Elements3_regions.bed example/Feature1.bed example/Feature2.bed example/features.header.bed.txt example/regions.header.txt |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ._loadandplot.R |
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| Binary file ._loadandplot.R has changed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ._plotwithscale.R |
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| Binary file ._plotwithscale.R has changed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ._testandplot.R |
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| Binary file ._testandplot.R has changed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/Control.bed --- a/ETn_example/Control.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/DESCRIPTION.txt --- a/ETn_example/DESCRIPTION.txt Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content". -In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding -fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream -of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements, -used as control in the test. The regions are aligned around their center (i.e. around the ETn integration -sites). -Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In -particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination -hotspots curve made of 64 values. The measurement used is the feature content, i.e. the -fraction of the 1-kb window that is covered by recombination hotspots - -Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F -Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse -endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology. -12(6): 1-41. -Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL -Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two -active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007. -Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams, -B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse -genome. Genetics. 191: 757-764. \ No newline at end of file |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/ETn_fixed.bed --- a/ETn_example/ETn_fixed.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1296 +0,0 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69758\t102433820\r\n-chr7\t110115837\t110185134\r\n-chr7\t110593609\t110657942\r\n-chr7\t111828298\t111892634\r\n-chr7\t113312731\t113382215\r\n-chr7\t113768856\t113840290\r\n-chr7\t115660728\t115732171\r\n-chr7\t117629868\t117694188\r\n-chr7\t120157418\t120221754\r\n-chr7\t121024547\t121088906\r\n-chr7\t125426839\t125490900\r\n-chr7\t127489003\t127553340\r\n-chr7\t130507539\t130571878\r\n-chr7\t134261471\t134325806\r\n-chr7\t138933955\t138998277\r\n-chr7\t139084737\t139149053\r\n-chr7\t140067401\t140131723\r\n-chr7\t140688526\t140759900\r\n-chr7\t143399593\t143469131\r\n-chr7\t145614147\t145678208\r\n-chr7\t147730581\t147794642\r\n-chr7\t149421578\t149485895\r\n-chr8\t3801027\t3865347\r\n-chr8\t4803179\t4867504\r\n-chr8\t7824324\t7888646\r\n-chr8\t15722072\t15793287\r\n-chr8\t18251757\t18315818\r\n-chr8\t18465381\t18529442\r\n-chr8\t19045164\t19112378\r\n-chr8\t22096250\t22137512\r\n-chr8\t24678842\t24743165\r\n-chr8\t25794478\t25858799\r\n-chr8\t26014127\t26078462\r\n-chr8\t26468922\t26533260\r\n-chr8\t28479149\t28543469\r\n-chr8\t30097851\t30161911\r\n-chr8\t30460129\t30524450\r\n-chr8\t30752787\t30817107\r\n-chr8\t31563440\t31627777\r\n-chr8\t36022443\t36086504\r\n-chr8\t36959548\t37023870\r\n-chr8\t39028207\t39092267\r\n-chr8\t41087234\t41151556\r\n-chr8\t41620051\t41689555\r\n-chr8\t42004143\t42068203\r\n-chr8\t43019118\t43083438\r\n-chr8\t47722042\t47786380\r\n-chr8\t59252906\t59322400\r\n-chr8\t60789544\t60853875\r\n-chr8\t61197366\t61261703\r\n-chr8\t61532874\t61596935\r\n-chr8\t63294270\t63358605\r\n-chr8\t64185293\t64253284\r\n-chr8\t64763207\t64827530\r\n-chr8\t67113241\t67177577\r\n-chr8\t69123511\t69187572\r\n-chr8\t70169472\t70233795\r\n-chr8\t72177196\t72241533\r\n-chr8\t75436025\t75500364\r\n-chr8\t76584577\t76648638\r\n-chr8\t77497140\t77561453\r\n-chr8\t77747147\t77811482\r\n-chr8\t79352165\t79416481\r\n-chr8\t80631654\t80703131\r\n-chr8\t83678886\t83743222\r\n-chr8\t87650996\t87722809\r\n-chr8\t88349042\t88413368\r\n-chr8\t94809868\t94874201\r\n-chr8\t95383980\t95448041\r\n-chr8\t102794796\t102859131\r\n-chr8\t103935008\t103999308\r\n-chr8\t109626938\t109691000\r\n-chr8\t109709405\t109773728\r\n-chr8\t116384465\t116448815\r\n-chr8\t120505951\t120570011\r\n-chr8\t121428979\t121493588\r\n-chr8\t125683558\t125747880\r\n-chr8\t128575325\t128644983\r\n-chr9\t4047472\t4116542\r\n-chr9\t4806803\t4870864\r\n-chr9\t4884580\t4954084\r\n-chr9\t6022806\t6092325\r\n-chr9\t6275883\t6339944\r\n-chr9\t7392890\t7457209\r\n-chr9\t7462474\t7526795\r\n-chr9\t7766967\t7837187\r\n-chr9\t8271124\t8335185\r\n-chr9\t8402204\t8466265\r\n-chr9\t8764452\t8828512\r\n-chr9\t11784168\t11855632\r\n-chr9\t12170129\t12234190\r\n-chr9\t12237687\t12309084\r\n-chr9\t12318611\t12382934\r\n-chr9\t12721775\t12785836\r\n-chr9\t13835575\t13899894\r\n-chr9\t15182924\t15247260\r\n-chr9\t17955775\t18020096\r\n-chr9\t18827860\t18898433\r\n-chr9\t24340641\t24404702\r\n-chr9\t24593904\t24658240\r\n-chr9\t27266534\t27330872\r\n-chr9\t30430874\t30495213\r\n-chr9\t35587912\t35657485\r\n-chr9\t35863647\t35935120\r\n-chr9\t37845538\t37909860\r\n-chr9\t38185239\t38249385\r\n-chr9\t38896815\t38961150\r\n-chr9\t41662492\t41726552\r\n-chr9\t43638042\t43702378\r\n-chr9\t45006098\t45070433\r\n-chr9\t47047851\t47112173\r\n-chr9\t49906212\t49970548\r\n-chr9\t50402386\t50472116\r\n-chr9\t52696613\t52760674\r\n-chr9\t53981007\t54045329\r\n-chr9\t55048978\t55113313\r\n-chr9\t55639453\t55703790\r\n-chr9\t57139057\t57203396\r\n-chr9\t58372958\t58437282\r\n-chr9\t59751834\t59816157\r\n-chr9\t59828617\t59892938\r\n-chr9\t67460563\t67524885\r\n-chr9\t69791346\t69855407\r\n-chr9\t72084500\t72148804\r\n-chr9\t73306304\t73370365\r\n-chr9\t75546159\t75615764\r\n-chr9\t76067163\t76131499\r\n-chr9\t78205560\t78269895\r\n-chr9\t79863716\t79932960\r\n-chr9\t83543186\t83607520\r\n-chr9\t83961391\t84025712\r\n-chr9\t84745537\t84816469\r\n-chr9\t87287487\t87351823\r\n-chr9\t88965683\t89029744\r\n-chr9\t89914557\t89978617\r\n-chr9\t95389913\t95454249\r\n-chr9\t98540578\t98604900\r\n-chr9\t104333243\t104397304\r\n-chr9\t105712170\t105776231\r\n-chr9\t105976408\t106040743\r\n-chr9\t108139205\t108203544\r\n-chr9\t111904500\t111968818\r\n-chr9\t113768402\t113832464\r\n-chr9\t120794546\t120858880\r\n-chr9\t122321963\t122386298\r\n' |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/Recombination_hotspots.txt --- a/ETn_example/Recombination_hotspots.txt Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t110616374\t110680374\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.544\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t0.456\t0.544\t1\t1\t1\r\n-chr9\t111968818\t112032818\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t113836504\t113900504\t0\t0\t0.457\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\r\n-chr9\t118910538\t118974538\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.491\t1\t1\t1\t1\t1\t1\t1\t1\t0.509\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t121627136\t121691136\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/features.header --- a/ETn_example/features.header Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -Recombination_hotspots.txt Recomb_hot Recombination hotspots \ No newline at end of file |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 ETn_example/regions.header --- a/ETn_example/regions.header Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Control.bed Control Control -ETn_fixed.bed ETn_fixed ETn fixed \ No newline at end of file |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Controls_regions.bed --- a/example/Controls_regions.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,35 +0,0 @@ -chr1 91399892 91499892 -chr1 116447079 116547079 -chr2 231381109 231481109 -chr3 47386633 47486633 -chr3 99195712 99295712 -chr3 116765114 116865114 -chr3 134345017 134445017 -chr4 68064019 68164019 -chr4 137465811 137565811 -chr4 173293016 173393016 -chr5 59044110 59144110 -chr5 94592763 94692763 -chr5 108436006 108536006 -chr5 110836898 110936898 -chr5 146661073 146761073 -chr6 99727306 99827306 -chr7 88291325 88391325 -chr7 120999784 121099784 -chr8 126860366 126960366 -chr8 127636547 127736547 -chr11 41362564 41462564 -chr11 101741527 101841527 -chr12 15210277 15310277 -chr13 91106037 91206037 -chr13 91518822 91618822 -chr13 98959030 99059030 -chr15 39087176 39187176 -chr17 58542142 58642142 -chr18 12199823 12299823 -chr20 8173704 8273704 -chr21 16255112 16355112 -chr21 45089115 45189115 -chrX 23898983 23998983 -chrX 37029585 37129585 -chrX 103593349 103693349 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/DESCRIPTION.txt --- a/example/DESCRIPTION.txt Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", -corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control". |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Elements1_regions.bed --- a/example/Elements1_regions.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -chr2 49960150 50060150 -chr2 55912445 56012445 -chr3 140326750 140426750 -chr4 41772201 41872201 -chr4 70629719 70729719 -chr4 109340735 109440735 -chr5 15025389 15125389 -chr5 43028888 43128888 -chr5 58231354 58331354 -chr5 91277761 91377761 -chr5 119464508 119564508 -chr6 85309170 85409170 -chr6 85762072 85862072 -chr6 134621363 134721363 -chr6 147470164 147570164 -chr7 77195798 77295798 -chr7 77880914 77980914 -chr7 114805399 114905399 -chr10 46350885 46450885 -chr10 67833078 67933078 -chr12 27722692 27822692 -chr12 95518506 95618506 -chr12 117863466 117963466 -chr14 100464166 100564166 -chrX 29266748 29366748 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Elements2_regions.bed --- a/example/Elements2_regions.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ -chr1 65942901 66042901 -chr1 117128102 117228102 -chr1 190338169 190438169 -chr2 227365478 227465478 -chr6 50856764 50956764 -chr6 135703067 135803067 -chr7 38228726 38328726 -chr7 51115898 51215898 -chr7 150325760 150425760 -chr8 25475691 25575691 -chr9 73374609 73474609 -chr11 55092625 55192625 -chr11 86581661 86681661 -chr12 12795284 12895284 -chr12 48151882 48251882 -chr12 83109951 83209951 -chr15 31430278 31530278 -chr15 65610815 65710815 -chr17 40766223 40866223 -chr20 17245048 17345048 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Elements3_regions.bed --- a/example/Elements3_regions.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -chr1 49721616 49821616 -chr1 95059425 95159425 -chr1 207236313 207336313 -chr2 73790843 73890843 -chr3 134465321 134565321 -chr4 43433669 43533669 -chr4 122032777 122132777 -chr5 12701747 12801747 -chr5 58501529 58601529 -chr5 152853250 152953250 -chr6 136085023 136185023 -chr6 147019529 147119529 -chr7 14192964 14292964 -chr7 125519883 125619883 -chr8 77652872 77752872 -chr8 108375665 108475665 -chr9 2984971 3084971 -chr10 978822 1078822 -chr11 18395046 18495046 -chr12 47273592 47373592 -chr12 60095778 60195778 -chr12 84854096 84954096 -chr12 95157539 95257539 -chr14 23982000 24082000 -chr16 1875335 1975335 -chr16 66789863 66889863 -chr18 64644131 64744131 -chr21 15966609 16066609 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Feature1.bed --- a/example/Feature1.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 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|
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/Feature2.bed --- a/example/Feature2.bed Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 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31\t64682131\t5.19535591598228\n-chr18\t64682131\t64684131\t6.0555950876448\n-chr18\t64684131\t64686131\t3.54284284855037\n-chr18\t64686131\t64688131\t5.0657204197487\n-chr18\t64688131\t64690131\t4.61156619971275\n-chr18\t64690131\t64692131\t4.66622025797826\n-chr18\t64692131\t64694131\t5.34521271919367\n-chr18\t64694131\t64696131\t9.87597953863361\n-chr18\t64696131\t64698131\t7.05091406041253\n-chr18\t64698131\t64700131\t8.00182216055189\n-chr18\t64700131\t64702131\t7.91390780851007\n-chr18\t64702131\t64704131\t6.60478767008177\n-chr18\t64704131\t64706131\t8.42205253797048\n-chr18\t64706131\t64708131\t8.4092636416611\n-chr18\t64708131\t64710131\t7.33893411142367\n-chr18\t64710131\t64712131\t6.44977234209029\n-chr18\t64712131\t64714131\t6.14212509408095\n-chr18\t64714131\t64716131\t7.33470365201403\n-chr18\t64716131\t64718131\t6.14466300830508\n-chr18\t64718131\t64720131\t6.28759018496124\n-chr18\t64720131\t64722131\t6.13121264285508\n-chr18\t64722131\t64724131\t6.25464222302313\n-chr18\t64724131\t64726131\t6.22857474092805\n-chr18\t64726131\t64728131\t6.7164061474755\n-chr18\t64728131\t64730131\t7.71694797882967\n-chr18\t64730131\t64732131\t6.47134532938063\n-chr18\t64732131\t64734131\t5.44078856911433\n-chr18\t64734131\t64736131\t6.72171185147245\n-chr18\t64736131\t64738131\t7.45623695140267\n-chr18\t64738131\t64740131\t6.66053173863693\n-chr18\t64740131\t64742131\t7.26582262622926\n-chr18\t64742131\t64744131\t7.26639325298473\n-chr21\t15966609\t15968609\t3.61661096782077\n-chr21\t15968609\t15970609\t4.73386208722406\n-chr21\t15970609\t15972609\t5.8015549021153\n-chr21\t15972609\t15974609\t4.96167153907388\n-chr21\t15974609\t15976609\t3.95102647749112\n-chr21\t15976609\t15978609\t3.97020922833049\n-chr21\t15978609\t15980609\t5.33786080501161\n-chr21\t15980609\t15982609\t4.36434578068312\n-chr21\t15982609\t15984609\t5.80198476623914\n-chr21\t15984609\t15986609\t5.35739211903602\n-chr21\t15986609\t15988609\t6.08746983525949\n-chr21\t15988609\t15990609\t4.34773396054126\n-chr21\t15990609\t15992609\t5.13949591522979\n-chr21\t15992609\t15994609\t3.73402272260864\n-chr21\t15994609\t15996609\t5.39450798275315\n-chr21\t15996609\t15998609\t5.55466043086729\n-chr21\t15998609\t16000609\t5.28998031818056\n-chr21\t16000609\t16002609\t6.19329925730006\n-chr21\t16002609\t16004609\t2.67150074437477\n-chr21\t16004609\t16006609\t5.16423939358034\n-chr21\t16006609\t16008609\t4.69609507505699\n-chr21\t16008609\t16010609\t5.44942073640721\n-chr21\t16010609\t16012609\t6.03847400860453\n-chr21\t16012609\t16014609\t5.97649168698122\n-chr21\t16014609\t16016609\t5.36013704359642\n-chr21\t16016609\t16018609\t7.92817462773764\n-chr21\t16018609\t16020609\t7.69377454814871\n-chr21\t16020609\t16022609\t8.80647396276848\n-chr21\t16022609\t16024609\t8.52452119781362\n-chr21\t16024609\t16026609\t7.89462789559928\n-chr21\t16026609\t16028609\t6.13805198380259\n-chr21\t16028609\t16030609\t4.64531272265593\n-chr21\t16030609\t16032609\t6.29826676008479\n-chr21\t16032609\t16034609\t7.79487866360525\n-chr21\t16034609\t16036609\t7.31994055340419\n-chr21\t16036609\t16038609\t8.8004479775322\n-chr21\t16038609\t16040609\t8.25854856063076\n-chr21\t16040609\t16042609\t5.04576860851306\n-chr21\t16042609\t16044609\t7.30730130969012\n-chr21\t16044609\t16046609\t7.83870783306589\n-chr21\t16046609\t16048609\t7.63074529828173\n-chr21\t16048609\t16050609\t6.43100021814285\n-chr21\t16050609\t16052609\t7.27551387601485\n-chr21\t16052609\t16054609\t6.26545170591659\n-chr21\t16054609\t16056609\t7.12562466213381\n-chr21\t16056609\t16058609\t6.26895239202312\n-chr21\t16058609\t16060609\t7.3992370168724\n-chr21\t16060609\t16062609\t7.97487587946482\n-chr21\t16062609\t16064609\t6.76355670816454\n-chr21\t16064609\t16066609\t6.11742019669001\n' |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/features.header.bed.txt --- a/example/features.header.bed.txt Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -Feature1.bed ftr1 Feature 1 -Feature2.bed ftr2 Feature 2 \ No newline at end of file |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 example/regions.header.txt --- a/example/regions.header.txt Wed May 31 16:26:29 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -Elements1_regions.bed elem1 Elements 1 -Elements2_regions.bed elem2 Elements 2 -Elements3_regions.bed elem3 Elements 3 -Controls_regions.bed control Controls \ No newline at end of file |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 loadandplot.xml --- a/loadandplot.xml Wed May 31 16:26:29 2017 -0400 +++ b/loadandplot.xml Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -232,6 +232,30 @@ <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" /> </outputs> + <tests> + <test> + <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" /> + <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" /> + <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" /> + <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" /> + <param name="zerobased" value="TRUE" /> + <param name="smoothing" value="kernel" /> + <param name="alignment" value="center" /> + <param name="kernelbandwidth" value="5" /> + <param name="fillgaps" value="TRUE" /> + <param name="average" value="TRUE" /> + <param name="size" value="TRUE" /> + <param name="plottype" value="boxplot" /> + <param name="prob0" value="0.25" /> + <param name="prob1" value="0.5" /> + <param name="prob2" value="0.75" /> + <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" /> + <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" /> + <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" /> + <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" /> + </test> + </tests> + <help> This tool imports a collection of genomic region datasets, and associates to each region multiple genomic feature measurements. It allows to align the regions in multiple ways |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 plotwithscale.xml --- a/plotwithscale.xml Wed May 31 16:26:29 2017 -0400 +++ b/plotwithscale.xml Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -132,12 +132,43 @@ </inputs> <outputs> - <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />--> - <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" /> - <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" /> - <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" /> + <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />--> + <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" /> + <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" /> + <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" /> </outputs> + <tests> + <test> + <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" /> + <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" /> + <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" /> + <repeat name="thresholdontestscale"> + <param name="test" value="1" /> + <param name="feature" value="1" /> + <param name="scale" value="10" /> + </repeat> + <repeat name="thresholdontestscale"> + <param name="test" value="1,2,3" /> + <param name="feature" value="2" /> + <param name="scale" value="20" /> + </repeat> + <param name="alpha" value="0.05" /> + <param name="average" value="TRUE" /> + <param name="size" value="TRUE" /> + <param name="plottype" value="boxplot" /> + <param name="prob0" value="0.25" /> + <param name="prob1" value="0.5" /> + <param name="prob2" value="0.75" /> + <param name="groupby" value="feature" /> + <param name="featurealphaplot" value="0.05" /> + <param name="featureonlysig" value="TRUE" /> + <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" /> + <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" /> + <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" /> + </test> + </tests> + <help> This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves for the different tests performed at the selected scale, and it creates a graphical representation of the |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/._.DS_Store |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/._Elements1_regions.bed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/._Feature1.bed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/._regions.header.txt |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Controls_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Controls_regions.bed Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,35 @@ +chr1 91399892 91499892 +chr1 116447079 116547079 +chr2 231381109 231481109 +chr3 47386633 47486633 +chr3 99195712 99295712 +chr3 116765114 116865114 +chr3 134345017 134445017 +chr4 68064019 68164019 +chr4 137465811 137565811 +chr4 173293016 173393016 +chr5 59044110 59144110 +chr5 94592763 94692763 +chr5 108436006 108536006 +chr5 110836898 110936898 +chr5 146661073 146761073 +chr6 99727306 99827306 +chr7 88291325 88391325 +chr7 120999784 121099784 +chr8 126860366 126960366 +chr8 127636547 127736547 +chr11 41362564 41462564 +chr11 101741527 101841527 +chr12 15210277 15310277 +chr13 91106037 91206037 +chr13 91518822 91618822 +chr13 98959030 99059030 +chr15 39087176 39187176 +chr17 58542142 58642142 +chr18 12199823 12299823 +chr20 8173704 8273704 +chr21 16255112 16355112 +chr21 45089115 45189115 +chrX 23898983 23998983 +chrX 37029585 37129585 +chrX 103593349 103693349 |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Elements1_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Elements1_regions.bed Thu Jun 08 16:44:13 2017 -0400 |
| b |
| @@ -0,0 +1,25 @@ +chr2 49960150 50060150 +chr2 55912445 56012445 +chr3 140326750 140426750 +chr4 41772201 41872201 +chr4 70629719 70729719 +chr4 109340735 109440735 +chr5 15025389 15125389 +chr5 43028888 43128888 +chr5 58231354 58331354 +chr5 91277761 91377761 +chr5 119464508 119564508 +chr6 85309170 85409170 +chr6 85762072 85862072 +chr6 134621363 134721363 +chr6 147470164 147570164 +chr7 77195798 77295798 +chr7 77880914 77980914 +chr7 114805399 114905399 +chr10 46350885 46450885 +chr10 67833078 67933078 +chr12 27722692 27822692 +chr12 95518506 95618506 +chr12 117863466 117963466 +chr14 100464166 100564166 +chrX 29266748 29366748 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Elements2_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Elements2_regions.bed Thu Jun 08 16:44:13 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +chr1 65942901 66042901 +chr1 117128102 117228102 +chr1 190338169 190438169 +chr2 227365478 227465478 +chr6 50856764 50956764 +chr6 135703067 135803067 +chr7 38228726 38328726 +chr7 51115898 51215898 +chr7 150325760 150425760 +chr8 25475691 25575691 +chr9 73374609 73474609 +chr11 55092625 55192625 +chr11 86581661 86681661 +chr12 12795284 12895284 +chr12 48151882 48251882 +chr12 83109951 83209951 +chr15 31430278 31530278 +chr15 65610815 65710815 +chr17 40766223 40866223 +chr20 17245048 17345048 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Elements3_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Elements3_regions.bed Thu Jun 08 16:44:13 2017 -0400 |
| b |
| @@ -0,0 +1,28 @@ +chr1 49721616 49821616 +chr1 95059425 95159425 +chr1 207236313 207336313 +chr2 73790843 73890843 +chr3 134465321 134565321 +chr4 43433669 43533669 +chr4 122032777 122132777 +chr5 12701747 12801747 +chr5 58501529 58601529 +chr5 152853250 152953250 +chr6 136085023 136185023 +chr6 147019529 147119529 +chr7 14192964 14292964 +chr7 125519883 125619883 +chr8 77652872 77752872 +chr8 108375665 108475665 +chr9 2984971 3084971 +chr10 978822 1078822 +chr11 18395046 18495046 +chr12 47273592 47373592 +chr12 60095778 60195778 +chr12 84854096 84954096 +chr12 95157539 95257539 +chr14 23982000 24082000 +chr16 1875335 1975335 +chr16 66789863 66889863 +chr18 64644131 64744131 +chr21 15966609 16066609 |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Feature1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Feature1.bed Thu Jun 08 16:44:13 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 @@\n+chr1\t91399892\t91401892\t0.914729028492568\n+chr1\t91401892\t91403892\t1.03788669317729\n+chr1\t91403892\t91405892\t1.15695078809331\n+chr1\t91405892\t91407892\t1.05433971377051\n+chr1\t91407892\t91409892\t1.05827244724317\n+chr1\t91409892\t91411892\t1.00216117481117\n+chr1\t91411892\t91413892\t0.873489001753337\n+chr1\t91413892\t91415892\t0.873100412116323\n+chr1\t91415892\t91417892\t0.928712683217515\n+chr1\t91417892\t91419892\t0.94132562114723\n+chr1\t91419892\t91421892\t1.06739894033636\n+chr1\t91421892\t91423892\t0.909275169317382\n+chr1\t91423892\t91425892\t1.10093887463398\n+chr1\t91425892\t91427892\t1.05342912580018\n+chr1\t91427892\t91429892\t0.970074712768588\n+chr1\t91429892\t91431892\t0.742552329847752\n+chr1\t91431892\t91433892\t1.09649292566553\n+chr1\t91433892\t91435892\t0.902578291528885\n+chr1\t91435892\t91437892\t0.821718064516058\n+chr1\t91437892\t91439892\t0.909063175846949\n+chr1\t91439892\t91441892\t1.12598647717153\n+chr1\t91441892\t91443892\t0.962991989888592\n+chr1\t91443892\t91445892\t0.886361985680751\n+chr1\t91445892\t91447892\t1.19735794895968\n+chr1\t91447892\t91449892\t1.1058589065373\n+chr1\t91449892\t91451892\t1.11830938343819\n+chr1\t91451892\t91453892\t0.891849450289035\n+chr1\t91453892\t91455892\t0.921613352575372\n+chr1\t91455892\t91457892\t0.961394603438276\n+chr1\t91457892\t91459892\t0.942120540462845\n+chr1\t91459892\t91461892\t1.04179227745858\n+chr1\t91461892\t91463892\t0.846036296260439\n+chr1\t91463892\t91465892\t0.903782108017989\n+chr1\t91465892\t91467892\t0.926324469715607\n+chr1\t91467892\t91469892\t1.01617788108211\n+chr1\t91469892\t91471892\t1.01871994841433\n+chr1\t91471892\t91473892\t0.86346600407464\n+chr1\t91473892\t91475892\t0.911534382002842\n+chr1\t91475892\t91477892\t0.909397860657818\n+chr1\t91477892\t91479892\t0.882437981483481\n+chr1\t91479892\t91481892\t1.20022730271379\n+chr1\t91481892\t91483892\t1.02286707465404\n+chr1\t91483892\t91485892\t1.00824959158441\n+chr1\t91485892\t91487892\t1.13387236604912\n+chr1\t91487892\t91489892\t0.917808428397605\n+chr1\t91489892\t91491892\t1.00980153326694\n+chr1\t91491892\t91493892\t1.0780078042687\n+chr1\t91493892\t91495892\t1.05789211157318\n+chr1\t91495892\t91497892\t0.983519376160091\n+chr1\t91497892\t91499892\t1.06301499098899\n+chr1\t116447079\t116449079\t0.909510507890661\n+chr1\t116449079\t116451079\t1.04923486926106\n+chr1\t116451079\t116453079\t0.972429435962863\n+chr1\t116453079\t116455079\t0.94348509718749\n+chr1\t116455079\t116457079\t0.877213727110183\n+chr1\t116457079\t116459079\t1.07609955711144\n+chr1\t116459079\t116461079\t1.05964706503259\n+chr1\t116461079\t116463079\t1.08048074104999\n+chr1\t116463079\t116465079\t1.10397643608295\n+chr1\t116465079\t116467079\t0.879172377236955\n+chr1\t116467079\t116469079\t0.952455624542298\n+chr1\t116469079\t116471079\t0.872450868701435\n+chr1\t116471079\t116473079\t0.734632500870684\n+chr1\t116473079\t116475079\t0.975852194327443\n+chr1\t116475079\t116477079\t1.15968481779916\n+chr1\t116477079\t116479079\t1.03479249038231\n+chr1\t116479079\t116481079\t0.958716780567544\n+chr1\t116481079\t116483079\t1.00882150410174\n+chr1\t116483079\t116485079\t0.894048456447358\n+chr1\t116485079\t116487079\t0.862250242465922\n+chr1\t116487079\t116489079\t1.08563273479841\n+chr1\t116489079\t116491079\t1.03570610668607\n+chr1\t116491079\t116493079\t1.282637134762\n+chr1\t116493079\t116495079\t1.05344881721884\n+chr1\t116495079\t116497079\t0.958843714832433\n+chr1\t116497079\t116499079\t0.907730747212707\n+chr1\t116499079\t116501079\t0.964823764805327\n+chr1\t116501079\t116503079\t0.972508803669119\n+chr1\t116503079\t116505079\t0.964761127498888\n+chr1\t116505079\t116507079\t1.21022463445566\n+chr1\t116507079\t116509079\t0.870817357520223\n+chr1\t116509079\t116511079\t0.970216007864307\n+chr1\t116511079\t116513079\t1.09860269791989\n+chr1\t116513079\t116515079\t1.01985884672516\n+chr1\t116515079\t116517079\t1.04151199469522\n+chr1\t116517079\t116519079\t1.10542491108645\n+chr1\t116519079\t116521079\t1.06697958402493\n+chr1\t116521079\t116523079\t0.972137682316022\n+chr1\t116523079\t116525079\t0.900068042346903\n+chr1\t116525079\t116527079\t1.00945179072767\n+chr1\t116527079\t116529079\t0.910760202377398\n+chr1\t116529079\t116531079\t0.960315923931081\n+chr1\t116531079\t116533079\t1.05558603806716\n+chr1\t116533079\t116535079\t0.92038544115'..b'1\t64656131\t0.97369678388939\n+chr18\t64656131\t64658131\t0.910087798040937\n+chr18\t64658131\t64660131\t0.946468289624316\n+chr18\t64660131\t64662131\t1.05842665628809\n+chr18\t64662131\t64664131\t0.927667349376235\n+chr18\t64664131\t64666131\t1.18742333150313\n+chr18\t64666131\t64668131\t1.22205250380213\n+chr18\t64668131\t64670131\t0.880563425486305\n+chr18\t64670131\t64672131\t0.914485239144026\n+chr18\t64672131\t64674131\t1.01034737175594\n+chr18\t64674131\t64676131\t1.62264521151304\n+chr18\t64676131\t64678131\t1.48296645852995\n+chr18\t64678131\t64680131\t1.28681962535927\n+chr18\t64680131\t64682131\t1.53492939742228\n+chr18\t64682131\t64684131\t1.58844790171606\n+chr18\t64684131\t64686131\t1.49033262314301\n+chr18\t64686131\t64688131\t1.31424965988202\n+chr18\t64688131\t64690131\t1.45337032575317\n+chr18\t64690131\t64692131\t1.35217898213701\n+chr18\t64692131\t64694131\t1.77532370910719\n+chr18\t64694131\t64696131\t1.60398303218395\n+chr18\t64696131\t64698131\t1.69307164801575\n+chr18\t64698131\t64700131\t1.54229556388787\n+chr18\t64700131\t64702131\t1.68106575665579\n+chr18\t64702131\t64704131\t1.48714225361666\n+chr18\t64704131\t64706131\t1.55224087444918\n+chr18\t64706131\t64708131\t1.3662045024589\n+chr18\t64708131\t64710131\t1.57624355139023\n+chr18\t64710131\t64712131\t1.44378437443185\n+chr18\t64712131\t64714131\t1.37811537520723\n+chr18\t64714131\t64716131\t1.06551636789331\n+chr18\t64716131\t64718131\t1.04029846172777\n+chr18\t64718131\t64720131\t1.1012560789095\n+chr18\t64720131\t64722131\t1.16248797408295\n+chr18\t64722131\t64724131\t1.10209650363972\n+chr18\t64724131\t64726131\t1.12702540883185\n+chr18\t64726131\t64728131\t1.06158233209566\n+chr18\t64728131\t64730131\t1.24500209867534\n+chr18\t64730131\t64732131\t0.834309455846338\n+chr18\t64732131\t64734131\t0.757289730474966\n+chr18\t64734131\t64736131\t1.10451816307643\n+chr18\t64736131\t64738131\t0.92262846294503\n+chr18\t64738131\t64740131\t0.804253155660302\n+chr18\t64740131\t64742131\t1.00162039935745\n+chr18\t64742131\t64744131\t0.956034285823398\n+chr21\t15966609\t15968609\t1.12440801594939\n+chr21\t15968609\t15970609\t0.958928874609379\n+chr21\t15970609\t15972609\t0.980859325447667\n+chr21\t15972609\t15974609\t0.985836855465142\n+chr21\t15974609\t15976609\t0.924304227149342\n+chr21\t15976609\t15978609\t0.981319441090073\n+chr21\t15978609\t15980609\t0.949853799394529\n+chr21\t15980609\t15982609\t0.858050928062694\n+chr21\t15982609\t15984609\t0.836178837413462\n+chr21\t15984609\t15986609\t1.20633196613812\n+chr21\t15986609\t15988609\t0.969230627046025\n+chr21\t15988609\t15990609\t1.06120061342825\n+chr21\t15990609\t15992609\t0.88573302960608\n+chr21\t15992609\t15994609\t0.987056692659576\n+chr21\t15994609\t15996609\t1.05266019775439\n+chr21\t15996609\t15998609\t1.29745136461899\n+chr21\t15998609\t16000609\t1.3631797211261\n+chr21\t16000609\t16002609\t1.58553521861437\n+chr21\t16002609\t16004609\t1.47800659441217\n+chr21\t16004609\t16006609\t1.75042011315262\n+chr21\t16006609\t16008609\t1.39329136735319\n+chr21\t16008609\t16010609\t1.57255744319984\n+chr21\t16010609\t16012609\t1.20929102513908\n+chr21\t16012609\t16014609\t1.53853232166312\n+chr21\t16014609\t16016609\t1.64985481461386\n+chr21\t16016609\t16018609\t1.59575749789367\n+chr21\t16018609\t16020609\t1.42205668994404\n+chr21\t16020609\t16022609\t1.66053802113289\n+chr21\t16022609\t16024609\t1.70386086339594\n+chr21\t16024609\t16026609\t1.73541878893467\n+chr21\t16026609\t16028609\t1.39682491364686\n+chr21\t16028609\t16030609\t1.43336589770868\n+chr21\t16030609\t16032609\t1.63386317242737\n+chr21\t16032609\t16034609\t1.53233925104548\n+chr21\t16034609\t16036609\t1.53952241603109\n+chr21\t16036609\t16038609\t1.28074961173938\n+chr21\t16038609\t16040609\t1.27922409248079\n+chr21\t16040609\t16042609\t0.962647373836482\n+chr21\t16042609\t16044609\t0.950807449539781\n+chr21\t16044609\t16046609\t1.19549845149275\n+chr21\t16046609\t16048609\t1.03462200267827\n+chr21\t16048609\t16050609\t0.952643344080609\n+chr21\t16050609\t16052609\t1.20946321219477\n+chr21\t16052609\t16054609\t0.965927027586426\n+chr21\t16054609\t16056609\t0.976116334675594\n+chr21\t16056609\t16058609\t1.07756004404963\n+chr21\t16058609\t16060609\t0.987244607153093\n+chr21\t16060609\t16062609\t1.04620355385428\n+chr21\t16062609\t16064609\t1.02761240862396\n+chr21\t16064609\t16066609\t0.870263755617609\n' |
| b |
| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/Feature2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/Feature2.bed Thu Jun 08 16:44:13 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 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31\t64682131\t5.19535591598228\n+chr18\t64682131\t64684131\t6.0555950876448\n+chr18\t64684131\t64686131\t3.54284284855037\n+chr18\t64686131\t64688131\t5.0657204197487\n+chr18\t64688131\t64690131\t4.61156619971275\n+chr18\t64690131\t64692131\t4.66622025797826\n+chr18\t64692131\t64694131\t5.34521271919367\n+chr18\t64694131\t64696131\t9.87597953863361\n+chr18\t64696131\t64698131\t7.05091406041253\n+chr18\t64698131\t64700131\t8.00182216055189\n+chr18\t64700131\t64702131\t7.91390780851007\n+chr18\t64702131\t64704131\t6.60478767008177\n+chr18\t64704131\t64706131\t8.42205253797048\n+chr18\t64706131\t64708131\t8.4092636416611\n+chr18\t64708131\t64710131\t7.33893411142367\n+chr18\t64710131\t64712131\t6.44977234209029\n+chr18\t64712131\t64714131\t6.14212509408095\n+chr18\t64714131\t64716131\t7.33470365201403\n+chr18\t64716131\t64718131\t6.14466300830508\n+chr18\t64718131\t64720131\t6.28759018496124\n+chr18\t64720131\t64722131\t6.13121264285508\n+chr18\t64722131\t64724131\t6.25464222302313\n+chr18\t64724131\t64726131\t6.22857474092805\n+chr18\t64726131\t64728131\t6.7164061474755\n+chr18\t64728131\t64730131\t7.71694797882967\n+chr18\t64730131\t64732131\t6.47134532938063\n+chr18\t64732131\t64734131\t5.44078856911433\n+chr18\t64734131\t64736131\t6.72171185147245\n+chr18\t64736131\t64738131\t7.45623695140267\n+chr18\t64738131\t64740131\t6.66053173863693\n+chr18\t64740131\t64742131\t7.26582262622926\n+chr18\t64742131\t64744131\t7.26639325298473\n+chr21\t15966609\t15968609\t3.61661096782077\n+chr21\t15968609\t15970609\t4.73386208722406\n+chr21\t15970609\t15972609\t5.8015549021153\n+chr21\t15972609\t15974609\t4.96167153907388\n+chr21\t15974609\t15976609\t3.95102647749112\n+chr21\t15976609\t15978609\t3.97020922833049\n+chr21\t15978609\t15980609\t5.33786080501161\n+chr21\t15980609\t15982609\t4.36434578068312\n+chr21\t15982609\t15984609\t5.80198476623914\n+chr21\t15984609\t15986609\t5.35739211903602\n+chr21\t15986609\t15988609\t6.08746983525949\n+chr21\t15988609\t15990609\t4.34773396054126\n+chr21\t15990609\t15992609\t5.13949591522979\n+chr21\t15992609\t15994609\t3.73402272260864\n+chr21\t15994609\t15996609\t5.39450798275315\n+chr21\t15996609\t15998609\t5.55466043086729\n+chr21\t15998609\t16000609\t5.28998031818056\n+chr21\t16000609\t16002609\t6.19329925730006\n+chr21\t16002609\t16004609\t2.67150074437477\n+chr21\t16004609\t16006609\t5.16423939358034\n+chr21\t16006609\t16008609\t4.69609507505699\n+chr21\t16008609\t16010609\t5.44942073640721\n+chr21\t16010609\t16012609\t6.03847400860453\n+chr21\t16012609\t16014609\t5.97649168698122\n+chr21\t16014609\t16016609\t5.36013704359642\n+chr21\t16016609\t16018609\t7.92817462773764\n+chr21\t16018609\t16020609\t7.69377454814871\n+chr21\t16020609\t16022609\t8.80647396276848\n+chr21\t16022609\t16024609\t8.52452119781362\n+chr21\t16024609\t16026609\t7.89462789559928\n+chr21\t16026609\t16028609\t6.13805198380259\n+chr21\t16028609\t16030609\t4.64531272265593\n+chr21\t16030609\t16032609\t6.29826676008479\n+chr21\t16032609\t16034609\t7.79487866360525\n+chr21\t16034609\t16036609\t7.31994055340419\n+chr21\t16036609\t16038609\t8.8004479775322\n+chr21\t16038609\t16040609\t8.25854856063076\n+chr21\t16040609\t16042609\t5.04576860851306\n+chr21\t16042609\t16044609\t7.30730130969012\n+chr21\t16044609\t16046609\t7.83870783306589\n+chr21\t16046609\t16048609\t7.63074529828173\n+chr21\t16048609\t16050609\t6.43100021814285\n+chr21\t16050609\t16052609\t7.27551387601485\n+chr21\t16052609\t16054609\t6.26545170591659\n+chr21\t16054609\t16056609\t7.12562466213381\n+chr21\t16056609\t16058609\t6.26895239202312\n+chr21\t16058609\t16060609\t7.3992370168724\n+chr21\t16060609\t16062609\t7.97487587946482\n+chr21\t16062609\t16064609\t6.76355670816454\n+chr21\t16064609\t16066609\t6.11742019669001\n' 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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/features.header.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/features.header.bed.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,2 @@ +Feature1.bed ftr1 Feature 1 +Feature2.bed ftr2 Feature 2 \ No newline at end of file |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/input/regions.header.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/regions.header.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,4 @@ +Elements1_regions.bed elem1 Elements 1 +Elements2_regions.bed elem2 Elements 2 +Elements3_regions.bed elem3 Elements 3 +Controls_regions.bed control Controls \ No newline at end of file |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_loadandplot/iwtomics.loadandplot.features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_loadandplot/iwtomics.loadandplot.features.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,1 @@ +ftr1 ftr2 |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_loadandplot/iwtomics.loadandplot.regions.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_loadandplot/iwtomics.loadandplot.regions.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,1 @@ +control elem1 elem2 elem3 |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,18 @@ +Test: elem1 vs control, on feature ftr1 +Scale 10 0.337 0.492 0.718 0.884 0.954 0.966 0.966 0.966 0.966 0.979 0.979 0.979 0.979 0.966 0.948 0.886 0.817 0.813 0.839 0.889 0.947 0.983 0.97 0.97 0.935 0.777 0.554 0.362 0.457 0.681 0.84 0.904 0.904 0.904 0.904 0.904 0.884 0.884 0.889 0.884 0.852 0.752 0.691 0.802 0.905 0.995 0.995 0.937 0.817 0.688 + +Test: elem1 vs control, on feature ftr2 +Scale 20 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 + +Test: elem2 vs control, on feature ftr1 +Scale 50 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 + +Test: elem2 vs control, on feature ftr2 +Scale 20 0.989 0.937 0.845 0.759 0.644 0.545 0.545 0.583 0.739 0.802 0.805 0.801 0.801 0.819 0.801 0.696 0.598 0.561 0.653 0.733 0.829 0.899 0.918 0.918 0.918 0.918 0.926 0.926 0.926 0.926 0.965 0.926 0.922 0.922 0.922 0.98 0.922 0.922 0.922 0.922 0.922 0.922 0.922 0.929 0.922 0.922 0.922 0.922 0.922 0.922 + +Test: elem3 vs control, on feature ftr1 +Scale 50 0.756 0.756 0.644 0.644 0.662 0.823 0.943 1 0.986 0.927 0.806 0.488 0.117 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.186 0.698 0.885 0.732 0.602 0.474 0.381 0.381 0.455 0.607 0.822 0.822 0.689 + +Test: elem3 vs control, on feature ftr2 +Scale 20 0.914 0.914 0.914 0.917 0.925 0.949 0.925 0.925 0.925 0.925 0.941 0.941 0.925 0.925 0.925 0.925 0.925 0.925 0.907 0.9 0.9 0.9 0.792 0.181 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 + |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.RData |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt Thu Jun 08 16:44:13 2017 -0400 |
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| b'@@ -0,0 +1,312 @@\n+Test: elem1 vs control, on feature ftr1\n+Scale 50\t0.706\t0.806\t0.903\t0.945\t0.954\t0.966\t0.966\t0.966\t0.966\t0.979\t0.979\t0.979\t0.979\t0.966\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.983\t0.97\t0.97\t0.954\t0.943\t0.863\t0.808\t0.808\t0.808\t0.855\t0.904\t0.904\t0.904\t0.904\t0.904\t0.884\t0.884\t0.889\t0.884\t0.867\t0.867\t0.867\t0.867\t0.905\t0.995\t0.995\t0.937\t0.867\t0.827\n+Scale 49\t0.706\t0.806\t0.903\t0.945\t0.954\t0.966\t0.966\t0.966\t0.966\t0.979\t0.979\t0.979\t0.979\t0.966\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.983\t0.97\t0.97\t0.954\t0.943\t0.863\t0.808\t0.808\t0.808\t0.855\t0.904\t0.904\t0.904\t0.904\t0.904\t0.884\t0.884\t0.889\t0.884\t0.867\t0.867\t0.867\t0.867\t0.905\t0.995\t0.995\t0.937\t0.867\t0.827\n+Scale 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38\t0.706\t0.806\t0.903\t0.945\t0.954\t0.966\t0.966\t0.966\t0.966\t0.979\t0.979\t0.979\t0.979\t0.966\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.954\t0.983\t0.97\t0.97\t0.954\t0.943\t0.863\t0.758\t0.758\t0.787\t0.855\t0.904\t0.904\t0.904\t0.904\t0.904\t0.884\t0.884\t0.889\t0.'..b'0.001\t0.001\t0.001\t0.001\n+Scale 13\t0.852\t0.852\t0.852\t0.882\t0.923\t0.949\t0.923\t0.923\t0.923\t0.923\t0.941\t0.941\t0.923\t0.923\t0.923\t0.923\t0.923\t0.92\t0.871\t0.841\t0.841\t0.835\t0.654\t0.092\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 12\t0.837\t0.837\t0.837\t0.863\t0.898\t0.949\t0.915\t0.915\t0.915\t0.915\t0.941\t0.941\t0.915\t0.915\t0.915\t0.915\t0.915\t0.893\t0.853\t0.832\t0.832\t0.819\t0.603\t0.078\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 11\t0.81\t0.81\t0.82\t0.853\t0.883\t0.949\t0.89\t0.89\t0.89\t0.89\t0.941\t0.941\t0.89\t0.89\t0.89\t0.89\t0.895\t0.878\t0.842\t0.818\t0.813\t0.774\t0.562\t0.07\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 10\t0.778\t0.778\t0.802\t0.838\t0.883\t0.949\t0.883\t0.883\t0.883\t0.883\t0.941\t0.941\t0.883\t0.88\t0.88\t0.88\t0.895\t0.878\t0.839\t0.798\t0.756\t0.732\t0.528\t0.064\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 9\t0.743\t0.743\t0.763\t0.827\t0.883\t0.949\t0.883\t0.883\t0.883\t0.883\t0.941\t0.941\t0.883\t0.88\t0.88\t0.88\t0.895\t0.878\t0.805\t0.737\t0.708\t0.708\t0.517\t0.051\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 8\t0.724\t0.724\t0.724\t0.782\t0.866\t0.949\t0.875\t0.875\t0.875\t0.88\t0.941\t0.941\t0.88\t0.88\t0.88\t0.88\t0.895\t0.858\t0.75\t0.697\t0.697\t0.697\t0.499\t0.038\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 7\t0.71\t0.71\t0.71\t0.731\t0.826\t0.949\t0.861\t0.861\t0.861\t0.88\t0.941\t0.941\t0.863\t0.863\t0.863\t0.863\t0.895\t0.801\t0.695\t0.685\t0.685\t0.685\t0.436\t0.029\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 6\t0.681\t0.671\t0.671\t0.695\t0.78\t0.949\t0.823\t0.823\t0.823\t0.88\t0.941\t0.941\t0.859\t0.82\t0.82\t0.824\t0.895\t0.74\t0.667\t0.667\t0.667\t0.632\t0.349\t0.023\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 5\t0.681\t0.622\t0.63\t0.669\t0.759\t0.949\t0.822\t0.767\t0.813\t0.88\t0.941\t0.941\t0.859\t0.801\t0.756\t0.824\t0.895\t0.74\t0.653\t0.634\t0.608\t0.545\t0.306\t0.015\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 4\t0.681\t0.622\t0.588\t0.655\t0.759\t0.949\t0.822\t0.734\t0.787\t0.88\t0.941\t0.941\t0.859\t0.773\t0.738\t0.824\t0.895\t0.74\t0.638\t0.569\t0.564\t0.545\t0.278\t0.009\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 3\t0.681\t0.622\t0.588\t0.599\t0.759\t0.949\t0.822\t0.726\t0.706\t0.88\t0.941\t0.941\t0.859\t0.672\t0.738\t0.824\t0.895\t0.74\t0.567\t0.512\t0.564\t0.545\t0.234\t0.006\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 2\t0.681\t0.622\t0.5\t0.5\t0.717\t0.949\t0.822\t0.578\t0.586\t0.784\t0.941\t0.941\t0.759\t0.534\t0.611\t0.824\t0.895\t0.662\t0.45\t0.47\t0.564\t0.545\t0.158\t0.002\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+Scale 1\t0.681\t0.553\t0.434\t0.417\t0.582\t0.949\t0.66\t0.476\t0.513\t0.664\t0.889\t0.868\t0.592\t0.461\t0.487\t0.708\t0.895\t0.512\t0.342\t0.402\t0.564\t0.494\t0.074\t0.002\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\t0.001\n+\n' |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf |
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| Binary file test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf has changed |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,1 @@ +ftr1 ftr2 |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 test-data/output_testandplot/iwtomics.testandplot.tests.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_testandplot/iwtomics.testandplot.tests.txt Thu Jun 08 16:44:13 2017 -0400 |
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| @@ -0,0 +1,1 @@ +elem1 vs control elem2 vs control elem3 vs control |
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| diff -r 7698612e1dc7 -r 9ceb3ffcd817 testandplot.xml --- a/testandplot.xml Wed May 31 16:26:29 2017 -0400 +++ b/testandplot.xml Thu Jun 08 16:44:13 2017 -0400 |
| b |
| @@ -167,6 +167,45 @@ <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" /> </outputs> + <tests> + <test> + <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" /> + <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" /> + <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" /> + <repeat name="regions"> + <param name="region0" value="2" /> + <param name="region1" value="1" /> + </repeat> + <repeat name="regions"> + <param name="region0" value="3" /> + <param name="region1" value="1" /> + </repeat> + <repeat name="regions"> + <param name="region0" value="4" /> + <param name="region1" value="1" /> + </repeat> + <param name="featureslist" value="1,2" /> + <param name="statistics" value="mean" /> + <param name="permutations" value="1000" /> + <param name="alpha" value="0.05" /> + <param name="average" value="TRUE" /> + <param name="size" value="TRUE" /> + <param name="plottype" value="boxplot" /> + <param name="prob0" value="0.25" /> + <param name="prob1" value="0.5" /> + <param name="prob2" value="0.75" /> + <param name="groupby" value="feature" /> + <param name="featurealphaplot" value="0.05" /> + <param name="featureonlysig" value="TRUE" /> + <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" /> + <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" /> + <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" /> + <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" /> + <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" /> + <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" /> + </test> + </tests> + <help> This tool statistically evaluates differences in genomic features between groups of regions along the genome. In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise |