| Previous changeset 1:4ff502a46189 (2016-07-30) Next changeset 3:fa80bd02055f (2017-06-06) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79 |
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README.md biosigner_config.xml biosigner_wrapper.R |
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runit/NA runit/biosigner_runtests.R runit/biosigner_tests.R runit/output/information.txt runit/output/variableMetadata.tsv runit/sacurine/dataMatrix.tsv runit/sacurine/sampleMetadata.tsv runit/sacurine/variableMetadata.tsv |
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removed:
tests/biosigner_tests.R tests/sacurine/dataMatrix.tsv tests/sacurine/sampleMetadata.tsv tests/sacurine/variableMetadata.tsv |
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| diff -r 4ff502a46189 -r b2414be87d4b README.md --- a/README.md Sat Jul 30 12:21:07 2016 -0400 +++ b/README.md Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -1,14 +1,14 @@ Discovery of significant signatures from omics data =================================================== -A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure Status: [](https://travis-ci.org/workflow4metabolomics/biosigner). -## Description +### Description -**Version:** 2.2.4 -**Date:** 2016-07-30 +**Version:** 2.2.6 +**Date:** 2016-08-05 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. *Frontiers in Molecular Biosciences*, in review. @@ -16,31 +16,61 @@ **Reference history:** [W4M00003_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published) **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) -## Installation +### Installation -* Configuration file: `biosigner_config.xml`. +* Configuration file: `biosigner_config.xml` * Image files: - + `static/images/biosigner_workflowPositionImage.png`. - + `static/images/biosigner_workingExampleImage.png`. -* Wrapper file: `biosigner_wrapper.R`. -* R packages - + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. - + **biosigner** from Bioconductor (which itself depends on **ropls** from Bioconductor and **e1071** and **randomForest** from CRAN): `source("http://www.bioconductor.org/biocLite.R") ; biocLite("biosigner")`. + + `static/images/biosigner_workflowPositionImage.png` + + `static/images/biosigner_workingExampleImage.png` +* Wrapper file: `biosigner_wrapper.R` +* R packages + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + ``` + + **biosigner** from Bioconductor + + ```r + source("http://www.bioconductor.org/biocLite.R") + biocLite("biosigner") + ``` + +### Tests + +The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file -## Tests +You will need to install **RUnit** package in order to make it run: +```r +install.packages('RUnit', dependencies = TRUE) +``` -The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R +### Working example + +See the **W4M00001a_sacurine-subset-statistics** or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) -## News +### News + +###### CHANGES IN VERSION 2.2.6 -## CHANGES IN VERSION 2.2.4 +INTERNAL MODIFICATION + + * Minor internal modifications + +###### CHANGES IN VERSION 2.2.4 - * Internal updates for planemo and travis validation +INTERNAL MODIFICATION + + * Internal updates for planemo and travis validation -## CHANGES IN VERSION 2.2.2 +###### CHANGES IN VERSION 2.2.2 + +INTERNAL MODIFICATION * Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3) -## CHANGES IN VERSION 2.2.1 +###### CHANGES IN VERSION 2.2.1 + +NEW FEATURE * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0) |
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| diff -r 4ff502a46189 -r b2414be87d4b biosigner_config.xml --- a/biosigner_config.xml Sat Jul 30 12:21:07 2016 -0400 +++ b/biosigner_config.xml Sat Aug 06 12:17:12 2016 -0400 |
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| b'@@ -1,89 +1,92 @@\n-<tool id="biosigner" name="Biosigner" version="2.2.4">\n-\t<description>Molecular signature discovery from omics data</description>\n-\n-\t<requirements>\n-\t\t<requirement type="package" version="3.2.2">R</requirement>\n-\t\t<requirement type="package">r-batch</requirement>\n-\t\t<requirement type="package">bioconductor-biosigner</requirement>\n-\t</requirements>\n-\n-\t<command><![CDATA[\n-\t$__tool_directory__/biosigner_wrapper.R\n-\t\n-\t\tdataMatrix_in "$dataMatrix_in"\n-\t\tsampleMetadata_in "$sampleMetadata_in"\n-\t\tvariableMetadata_in "$variableMetadata_in"\n-\n-\t\trespC "$respC"\n-\t\t\n-\t\t#if $advCpt.opcC == "full"\n- methodC "$advCpt.methodC"\n- bootI "$advCpt.bootI"\n- tierC "$advCpt.tierC" \n- pvalN "$advCpt.pvalN"\n- seedI "$advCpt.seedI"\n-\t\t#end if\n-\n-\t\tvariableMetadata_out "$variableMetadata_out"\n-\t\tfigure_tier "$figure_tier"\n- figure_boxplot "$figure_boxplot"\n-\t\tinformation "$information"\n-\t\t]]></command>\n-\n-\t<inputs>\n-\t\t<param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: \'.\', missing: NA, mode: numerical, sep: tabular" />\n-\t\t<param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n-\t\t<param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: \'.\', missing: NA, mode: character and numerical, sep: tabular" />\n-\t\t<param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., \'case\' and \'control\')" />\t\n-\t\n-\t<conditional name="advCpt">\n-\t\t<param name="opcC" type="select" label="Advanced computational parameters" >\n-\t\t\t<option value="default" selected="true">Use default</option>\n-\t\t\t<option value="full">Full parameter list</option>\n-\t\t</param>\n-\t\t<when value="default"/>\n-\t\t<when value="full">\n- <param name="methodC" label="Classification method(s)" type="select" help="">\n- <option value="all" selected="true">all</option>\n- <option value="plsda">PLS-DA</option>\n- <option value="randomforest">Random Forest</option>\n- <option value="svm">SVM</option>\n- </param>\n-\t\t\t<param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/>\n- <param name="tierC" label="Selection tier(s)" type="select" help="">\n- <option value="S" selected="true">S</option>\n- <option value="A">S+A</option>\n- </param>\n- <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/>\n- <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/>\n-\t\t</when>\n-\t</conditional>\n-\t\t\n+<tool id="biosigner" name="Biosigner" version="2.2.6">\n+ <description>Molecular signature discovery from omics data</description>\n+ \n+ <requirements>\n+ <requirement type="package" version="3.2.2">R</requirement>\n+ <requirement type="package">r-batch</requirement>\n+ <requirement type="package">bioconductor-biosigner</requirement>\n+ </requirements>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+ \n+ <command><![CDATA[\n+ Rscript $__tool_directory__/biosigner_wrapper.R\n+ \n+ dataMatrix_in "$dataMatrix_in"\n+ sampleMetadata_in "$sampleMetadata_in"\n+ variableMetadata_in "$variableMetadata_in"\n+ \n+ respC "$respC"\n+ \n+ #if $advCpt.opcC == "full"\n+ methodC "$advCpt.methodC"\n+ bootI "$advCpt.bootI"\n+ tierC "$advCpt.tierC" \n+ pvalN "$advCpt.pvalN"\n+ seedI "$advCpt.seedI"\n+ #end if\n+ \n+ variableMetadata_out "$variableMetadata_out"\n+ figure_tier "$figure_tier"\n+ figure_boxplot "$figure_boxplot"\n+ information '..b'ta name="figure_boxplot" label="${tool.name}__figure-boxplot.pdf" format="pdf"/>\n-\t<data name="information" label="${tool.name}__information.txt" format="txt"/>\n+ <data name="information" label="${tool.name}__information.txt" format="txt"/>\n </outputs>\n \n <tests>\n-\t <test>\n-\t\t <param name="dataMatrix_in" value="dataMatrix.tsv"/>\n-\t\t <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>\n-\t\t <param name="variableMetadata_in" value="variableMetadata.tsv"/>\n-\t\t <param name="respC" value="gender"/>\n-\t\t <param name="opcC" value="full"/>\n-\t\t <param name="methodC" value="all"/>\n-\t\t <param name="bootI" value="5"/>\n-\t\t <param name="tierC" value="S"/>\n-\t\t <param name="pvalN" value="0.05"/>\n-\t\t <param name="seedI" value="123"/>\n-\t\t <output name="variableMetadata_out" file="variableMetadata.out"/>\n-\t </test>\n+ <test>\n+ <param name="dataMatrix_in" value="dataMatrix.tsv"/>\n+ <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>\n+ <param name="variableMetadata_in" value="variableMetadata.tsv"/>\n+ <param name="respC" value="gender"/>\n+ <param name="opcC" value="full"/>\n+ <param name="methodC" value="all"/>\n+ <param name="bootI" value="5"/>\n+ <param name="tierC" value="S"/>\n+ <param name="pvalN" value="0.05"/>\n+ <param name="seedI" value="123"/>\n+ <output name="variableMetadata_out" file="variableMetadata.out"/>\n+ </test>\n </tests>\n-\n+ \n <help>\t\n \n .. class:: infomark\n@@ -96,7 +99,7 @@\n \n **Please cite**\n \n-Philippe Rinaudo, Christophe Junot and Etienne A. Thevenot. *biosigner*: A new method for the discovery of restricted and stable molecular signatures from omics data. *submitted*.\n+Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2016). *biosigner*: a new method for the discovery of significant molecular signatures from omics data. *Frontiers in Molecular Biosciences*, **3** (http://dx.doi.org/10.3389/fmolb.2016.00026).\n \n ---------------------------------------------------\n \n@@ -104,7 +107,7 @@\n \n **R package**\n \n-The *biosigner* package has been submitted to the bioconductor repository (http://bioconductor.org/packages/biosigner).\n+The *biosigner* package is available from the bioconductor repository (http://bioconductor.org/packages/biosigner).\n \n ---------------------------------------------------\n \n@@ -243,7 +246,7 @@\n Working example\n ---------------\n \n-See the **W4M00003_diaplasma** in the **Shared Data/Published Histories** menu\n+See the **W4M00001a_sacurine-subset-statistics** and **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)\n \n \n \n@@ -259,18 +262,47 @@\n NEWS\n ----\n \n+CHANGES IN VERSION 2.2.6\n+========================\n+\n+INTERNAL MODIFICATIONS\n+\n+Minor internal modifications\n+\n+CHANGES IN VERSION 2.2.4\n+========================\n+\n+INTERNAL MODIFICATIONS\n+\n+Creating additional files for planemo and travis running and installation validation\n+\n CHANGES IN VERSION 2.2.2\n ========================\n \n+INTERNAL MODIFICATIONS\n+\n Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)\n \n CHANGES IN VERSION 2.2.1\n ========================\n \n+NEW FEATURE\n+\n Creation of the tool\n \n- </help>\n+</help>\n \n- <citations/>\n+<citations>\n+ <citation type="bibtex">@Article{Rinaudo2016,\n+ Title = {biosigner: a new method for the discovery of significant molecular signatures from omics data},\n+ Author = {Rinaudo, Philippe and Boudah, Samia and Junot, Christophe and Thevenot, Etienne A},\n+ Journal = {Frontiers in Molecular Biosciences},\n+ Year = {2016},\n+ Pages = {--},\n+ Volume = {3},\n+ Doi = {10.3389/fmolb.2016.00026}\n+ }</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+</citations>\n \n </tool>\n' |
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| diff -r 4ff502a46189 -r b2414be87d4b biosigner_wrapper.R --- a/biosigner_wrapper.R Sat Jul 30 12:21:07 2016 -0400 +++ b/biosigner_wrapper.R Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -5,9 +5,6 @@ argVc <- unlist(parseCommandArgs(evaluate=FALSE)) -#### Start_of_tested_code <- function() {} - - ##------------------------------ ## Initializing ##------------------------------ @@ -172,7 +169,8 @@ if(sum(tierMC %in% tierVc)) { cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "") print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), , - drop = FALSE]) + drop = FALSE]) + cat("\nAccuracy:\n") print(round(getAccuracyMN(bsnLs), 3)) } else @@ -222,9 +220,5 @@ options(stringsAsFactors = strAsFacL) - -#### End_of_tested_code <- function() {} - - rm(list = ls()) |
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| diff -r 4ff502a46189 -r b2414be87d4b runit/NA |
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| Binary file runit/NA has changed |
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| diff -r 4ff502a46189 -r b2414be87d4b runit/biosigner_runtests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/biosigner_runtests.R Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -0,0 +1,102 @@ +#!/usr/bin/env Rscript + +## Package +##-------- + +library(RUnit) + +## Constants +##---------- + +testOutDirC <- "output" +argVc <- commandArgs(trailingOnly = FALSE) +scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)]) + + +## Functions +##----------- + +## Reading tables (matrix or data frame) +readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) { + + file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\".")) + + switch(typeC, + matrix = return(t(as.matrix(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE)))), + dataframe = return(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE))) + +} + +## Call wrapper +wrapperCallF <- function(paramLs) { + + ## Set program path + wrapperPathC <- file.path(dirname(scriptPathC), "..", "biosigner_wrapper.R") + + ## Set arguments + argLs <- NULL + for (parC in names(paramLs)) + argLs <- c(argLs, parC, paramLs[[parC]]) + + ## Call + wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ") + + if(.Platform$OS.type == "windows") + wrapperCallC <- paste("Rscript", wrapperCallC) + + wrapperCodeN <- system(wrapperCallC) + + if (wrapperCodeN != 0) + stop("Error when running biosigner_wrapper.R.") + + ## Get output + outLs <- list() + if ("dataMatrix_out" %in% names(paramLs)) + outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix") + if ("sampleMetadata_out" %in% names(paramLs)) + outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe") + if ("variableMetadata_out" %in% names(paramLs)) + outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe") + if("information" %in% names(paramLs)) + outLs[["infVc"]] <- readLines(paramLs[["information"]]) + + return(outLs) +} + +## Setting default parameters +defaultArgF <- function(testInDirC) { + + defaultArgLs <- list() + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv"))) + defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv"))) + defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv"))) + defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv") + + defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv") + defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt") + + defaultArgLs + +} + +## Main +##----- + +## Create output folder +file.exists(testOutDirC) || dir.create(testOutDirC) + +## Run tests +test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$') +isValidTestSuite(test.suite) +test.results <- runTestSuite(test.suite) +print(test.results) |
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| diff -r 4ff502a46189 -r b2414be87d4b runit/biosigner_tests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/biosigner_tests.R Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -0,0 +1,15 @@ +test_sacurine_default <- function() { + + testDirC <- "sacurine" + argLs <- list(respC = "gender", + methodC = "all", + bootI = "5", + pvalN = "0.05", + seedI = "123") + + argLs <- c(defaultArgF(testDirC), argLs) + outLs <- wrapperCallF(argLs) + + checkEquals(outLs[["varDF"]]["Oxoglutaric acid", "gender_tier_S"], "plsda|randomforest|svm") + +} |
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| diff -r 4ff502a46189 -r b2414be87d4b runit/output/information.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/information.txt Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -0,0 +1,26 @@ + +Start of the 'Biosigner' Galaxy module call: Fri 05 Aug 2016 06:34:42 PM + +Significant features from 'S' tiers: + plsda randomforest svm +Oxoglutaric acid "S" "S" "S" +p-Anisic acid "S" "S" "S" +Testosterone glucuronide "S" "S" "S" +Pantothenic acid "S" "C" "B" +Acetylphenylalanine "S" "A" "E" +Malic acid "S" "A" "E" +alpha-N-Phenylacetyl-glutamine "S" "E" "E" +Citric acid "S" "E" "E" +Gluconic acid and/or isomers "S" "E" "E" +Glucuronic acid and/or isomers "S" "E" "E" +Hippuric acid "S" "E" "E" +Phe-Tyr-Asp (and isomers) "S" "E" "E" +Threonic acid/Erythronic acid "S" "E" "E" + +Accuracy: + plsda randomforest svm +Full 0.896 0.869 0.882 +AS 0.885 0.853 0.891 +S 0.864 0.866 0.882 + +End of 'Biosigner' Galaxy module call: 2016-08-05 18:34:54 |
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| diff -r 4ff502a46189 -r b2414be87d4b runit/output/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/variableMetadata.tsv Sat Aug 06 12:17:12 2016 -0400 |
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| @@ -0,0 +1,110 @@ +variableMetadata msiLevel hmdb chemicalClass gender_tier_S +(2-methoxyethoxy)propanoic acid isomer 2 Organi +(gamma)Glu-Leu/Ile 2 AA-pep +1-Methyluric acid 1 HMDB03099 AroHeP:Xenobi +1-Methylxanthine 1 HMDB10738 AroHeP +1,3-Dimethyluric acid 1 HMDB01857 AroHeP +1,7-Dimethyluric acid 1 HMDB11103 AroHeP +2-acetamido-4-methylphenyl acetate 2 AroHoM +2-Aminoadipic acid 1 HMDB00510 AA-pep +2-Hydroxybenzyl alcohol 1 HMDB59709 AroHoM +2-Isopropylmalic acid 1 HMDB00402 Organi +2-Methylhippuric acid 1 HMDB11723 AA-pep:AcyGly +2,2-Dimethylglutaric acid 1 Lipids +3-Hydroxybenzyl alcohol 1 HMDB59712 AroHoM +3-Hydroxyphenylacetic acid 1 HMDB00440 AroHoM +3-Indole carboxylic acid glucuronide 2 HMDB13189 Carboh +3-Methyl-2-oxovaleric acid 1 HMDB00491 Lipids +3-Methylcrotonylglycine 1 HMDB00459 AA-pep:AcyGly +3,3-Dimethylglutaric acid 1 HMDB02441 Lipids +3,4-Dihydroxybenzeneacetic acid 1 HMDB01336 AroHoM +3,5-dihydroxybenzoic acid/3,4-dihydroxybenzoic acid 2 AroHoM +3,7-Dimethyluric acid 1 HMDB01982 AroHeP +4-Acetamidobutanoic acid isomer 2 2 Lipids +4-Acetamidobutanoic acid isomer 3 2 Lipids +4-Hydroxybenzoic acid 1 HMDB00500 AroHoM +4-Methylhippuric acid/3-Methylhippuric acid 1 AA-pep:AcyGly +5-Hydroxyindoleacetic acid 1 HMDB00763 AroHeP +5-Sulfosalicylic acid 1 HMDB11725 AroHoM +6-(2-hydroxyethoxy)-6-oxohexanoic acid 2 Organi +6-(carboxymethoxy)-hexanoic acid 2 Organi +9-Methylxanthine 2 HMDB59716 AroHeP +Acetaminophen glucuronide 1 HMDB10316 Carboh +Acetylphenylalanine 1 HMDB00512 AA-pep plsda +alpha-N-Phenylacetyl-glutamine 1 HMDB06344 AA-pep plsda +Aminosalicyluric acid 2 AA-pep:AcyGly +Asp-Leu/Ile isomer 1 2 AA-pep +Asp-Leu/Ile isomer 2 2 AA-pep +Aspartic acid 1 HMDB00191 AA-pep +Azelaic acid 1 HMDB00784 Organi +Benzoic acid isomer 2 AroHoM +Chenodeoxycholic acid isomer 2 Lipids:Steroi +Cinnamoylglycine 1 HMDB11621 AA-pep:AcyGly +Citric acid 1 HMDB00094 Organi plsda +Dehydroepiandrosterone 3-glucuronide 1 HMDB10348 Lipids:Steroi +Dehydroepiandrosterone sulfate 1 HMDB01032 Lipids:Steroi +Deoxyhexose 1 HMDB00849 Carboh +Dimethylguanosine 2 HMDB04824 Nucleo +FMNH2 2 HMDB01142 AroHeP +Fumaric acid 1 HMDB00134 Lipids +Gentisic acid 1 HMDB00152 AroHoM +Glu-Val 2 HMDB59717 AA-pep +Gluconic acid and/or isomers 2 Carboh plsda +Glucuronic acid and/or isomers 2 Carboh plsda +Glyceric acid 1 HMDB00139 Carboh +Glycocholic acid isomer 2 2 Lipids:Steroi +Glycocholic acid isomer 3 2 Lipids:Steroi +Heptylmalonic acid 2 HMDB59719 Lipids +Hexanoylglycine 1 HMDB00701 AA-pep:AcyGly +Hippuric acid 1 HMDB00714 AA-pep:AcyGly plsda +Hydroxybenzyl alcohol isomer 2 AroHeM +Hydroxyphenyllactic acid 1 HMDB00755 AroHoM +Hydroxysuberic acid isomer 1 2 Organi +Hydroxysuberic acid isomer 2 2 Organi +Isovalerylalanine isomer 2 AA-pep +Ketoleucine 1 HMDB00695 Lipids +Kynurenic acid 1 HMDB00715 AA-pep +Malic acid 1 HMDB00156 Organi plsda +Methoxysalicylic acid isomer 2 AroHoM +Methyl (hydroxymethyl)pyrrolidine-carboxylate/Methyl (hydroxy)piperidine-carboxylate 2 AA-pep +Methylinosine 2 Nucleo +Mevalonic acid isomer 1 2 Organi +Monoethyl phthalate 2 HMDB02120 AroHoM:Xenobi +N-Acetyl-aspartic acid 1 HMDB00812 AA-pep +N-Acetylisoleucine 1 AA-pep +N-Acetylleucine 1 HMDB11756 AA-pep +N-Acetyltryptophan 1 HMDB13713 AA-pep +N-Acetyltryptophan isomer 3 2 AA-pep +N2-Acetylaminoadipic acid 2 AA-pep +N4-Acetylcytidine 1 HMDB05923 Nucleo +Nicotinuric acid isomer 2 AA-pep +Ortho-Hydroxyphenylacetic acid 1 HMDB00669 AroHoM +Oxoglutaric acid 2 HMDB00208 Organi plsda|randomforest|svm +p-Anisic acid 1 HMDB01101 AroHoM plsda|randomforest|svm +p-Hydroxyhippuric acid 2 HMDB13678 AA-pep:AcyGly +p-Hydroxymandelic acid 1 HMDB00822 AroHoM +p-Hydroxyphenylacetic acid 1 HMDB00020 AroHoM +Pantothenic acid 1 HMDB00210 AliAcy plsda +Pentose 2 Carboh +Phe-Tyr-Asp (and isomers) 2 AA-pep plsda +Porphobilinogen 1 HMDB00245 Organi +Pyridoxic acid isomer 1 2 AroHeM +Pyridylacetylglycine 2 HMDB59723 AA-pep:AcyGly:Xenobi +Pyrocatechol sulfate 2 HMDB59724 AroHoM +Pyroglutamic acid 1 HMDB00267 AliHeM +Pyrroledicarboxylic acid 2 AroHeM +Pyruvic acid 1 HMDB00243 Organi +Quinic acid 1 HMDB03072 AliHoM +Salicylic acid 1 HMDB01895 AroHoM:Xenobi +Sebacic acid 1 HMDB00792 Organi +Suberic acid 1 HMDB00893 Organi +Sulfosalicylic acid isomer 2 AroHoM +Taurine 1 HMDB00251 Organi +Testosterone glucuronide 2 HMDB03193 Lipids:Steroi plsda|randomforest|svm +Tetrahydrohippuric acid 2 AA-pep:AcyGly +Threo-3-Phenylserine 1 HMDB02184 AA-pep +Threonic acid/Erythronic acid 2 Carboh plsda +Tryptophan 1 HMDB00929 AA-pep +Valerylglycine isomer 1 2 AA-pep:AcyGly +Valerylglycine isomer 2 2 AA-pep:AcyGly +Xanthosine 1 HMDB00299 Nucleo |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b runit/sacurine/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/sacurine/dataMatrix.tsv Sat Aug 06 12:17:12 2016 -0400 |
| b |
| b'@@ -0,0 +1,110 @@\n+\tHU_011\tHU_014\tHU_015\tHU_017\tHU_018\tHU_019\tHU_020\tHU_021\tHU_022\tHU_023\tHU_024\tHU_025\tHU_026\tHU_027\tHU_028\tHU_029\tHU_030\tHU_031\tHU_032\tHU_033\tHU_034\tHU_035\tHU_036\tHU_037\tHU_038\tHU_039\tHU_040\tHU_041\tHU_042\tHU_043\tHU_044\tHU_045\tHU_046\tHU_047\tHU_048\tHU_049\tHU_050\tHU_051\tHU_052\tHU_053\tHU_054\tHU_055\tHU_056\tHU_057\tHU_058\tHU_060\tHU_061\tHU_062\tHU_063\tHU_064\tHU_065\tHU_066\tHU_067\tHU_068\tHU_069\tHU_070\tHU_072\tHU_073\tHU_074\tHU_075\tHU_076\tHU_077\tHU_078\tHU_079\tHU_080\tHU_081\tHU_082\tHU_083\tHU_084\tHU_085\tHU_086\tHU_087\tHU_088\tHU_089\tHU_090\tHU_091\tHU_092\tHU_093\tHU_094\tHU_095\tHU_097\tHU_098\tHU_099\tHU_100\tHU_101\tHU_102\tHU_103\tHU_105\tHU_106\tHU_107\tHU_108\tHU_109\tHU_110\tHU_112\tHU_113\tHU_114\tHU_115\tHU_116\tHU_117\tHU_118\tHU_119\tHU_120\tHU_121\tHU_122\tHU_123\tHU_124\tHU_125\tHU_126\tHU_127\tHU_129\tHU_130\tHU_131\tHU_132\tHU_133\tHU_134\tHU_135\tHU_136\tHU_137\tHU_138\tHU_139\tHU_140\tHU_142\tHU_143\tHU_144\tHU_145\tHU_146\tHU_147\tHU_148\tHU_149\tHU_150\tHU_152\tHU_154\tHU_155\tHU_156\tHU_157\tHU_158\tHU_159\tHU_160\tHU_162\tHU_163\tHU_164\tHU_166\tHU_167\tHU_168\tHU_169\tHU_170\tHU_171\tHU_172\tHU_173\tHU_174\tHU_175\tHU_177\tHU_179\tHU_180\tHU_181\tHU_182\tHU_183\tHU_184\tHU_185\tHU_186\tHU_187\tHU_188\tHU_189\tHU_190\tHU_191\tHU_192\tHU_193\tHU_194\tHU_195\tHU_196\tHU_197\tHU_198\tHU_199\tHU_200\tHU_201\tHU_202\tHU_203\tHU_204\tHU_205\tHU_206\tHU_207\tHU_208\tHU_209\n+(2-methoxyethoxy)propanoic acid isomer\t3.019766011\t3.81433889\t3.51969148\t2.56218265\t3.781921607\t4.161073524\t3.199174022\t3.378109516\t3.26452758\t3.787490017\t5.36371403\t3.202345706\t3.980345369\t3.020293232\t5.083462878\t3.388718935\t3.445549982\t1.27650453\t3.738547491\t1.253594534\t3.232847813\t4.559559002\t4.075948481\t2.570748216\t4.117811641\t5.038208548\t4.394350472\t3.665845239\t3.42296993\t3.74546685\t3.110957103\t4.252742233\t4.296284046\t2.995377877\t3.389971588\t5.349114655\t5.813374487\t4.304743135\t1.435768568\t5.369591232\t3.809431106\t3.0110849\t1.321147859\t3.401176446\t3.506978677\t5.24237122\t3.416889621\t3.415584225\t3.887678774\t3.555974489\t3.710985751\t4.232236312\t3.803661779\t4.379572071\t3.938310455\t1.376325833\t3.390271579\t5.215817481\t4.351838419\t3.714724817\t3.529736242\t3.862848205\t3.383427403\t3.661146136\t4.112188079\t4.249731699\t4.765467314\t3.51532253\t4.155850086\t4.045784307\t4.222815204\t4.168351191\t4.21782555\t3.612098315\t3.073157836\t4.235420499\t3.820636952\t2.797679916\t3.136688731\t3.665614604\t4.154569098\t4.299336631\t3.559309507\t2.996742676\t3.480758857\t4.034741661\t3.856739467\t2.852684744\t3.651373844\t3.759574346\t3.95537384\t2.849099312\t3.398179811\t3.984515153\t3.597414226\t3.290898684\t4.179746804\t4.943696911\t1.555387577\t3.60408986\t1.301552667\t3.640714337\t3.9838544\t3.827632696\t4.969533288\t3.504223072\t2.927962237\t4.011233932\t3.846480069\t3.945182011\t3.444671991\t3.617341684\t4.433665852\t3.758001601\t3.117921102\t3.604887175\t3.827127682\t1.270341972\t4.661967452\t3.058563173\t4.718036674\t3.77969937\t4.41111843\t3.735829951\t3.867366105\t3.377810236\t4.174630078\t4.051745447\t4.354188592\t3.522532268\t3.278058138\t3.375142493\t4.201257373\t3.531025311\t4.104608416\t3.308431289\t3.645655442\t5.077657223\t1.307713092\t4.169713633\t3.588749002\t3.785980907\t3.237049946\t4.089354447\t3.881406873\t3.732585337\t4.054073292\t4.137363308\t4.493012079\t4.930648019\t3.399303204\t3.372649157\t3.808510752\t3.912572116\t4.87526109\t3.423336878\t4.817034951\t3.574103433\t3.392706279\t3.640266302\t3.918027353\t2.984720403\t4.912949546\t3.391126097\t3.496992454\t4.454290676\t3.679442656\t4.082141098\t3.901748493\t4.459292151\t3.658028576\t3.61865837\t1.347192548\t3.156817506\t4.088827883\t3.68482537\t3.739437875\t3.62621039\t3.861325975\t1.321648909\t4.186987285\t3.748127215\t4.208859398\n+(gamma)Glu-Leu/Ile\t3.888479324\t4.277148905\t4.195649235\t4.323759965\t4.629328558\t4.412266289\t4.175236737\t4.635271487\t3.847144646\t3.871586241\t4.417740636\t4.328564559\t4.02953783\t4.152376569\t4.292682632\t4.531347748\t4.453076004\t4.6291358\t4.113221891\t4.150947299\t4.124072576\t3.901047415\t4.024811926\t4.181515516\t4.181368916\t3.876389846\t4.704956128\t4.21159738\t4.336920642\t4.38187405\t3.899552672\t4.061643136\t4.379398702\t3.828154643\t4.197557784\t4.015019635\t4.401325613\t3.802961064\t4.191430823\t4.'..b'049\t4.330382886\t4.100121431\t4.320047243\t4.239744811\t4.150606181\t4.124659917\t4.375400222\t4.251030211\t3.777775091\t4.361487807\t4.082842319\t4.083917302\t4.325269835\t4.010354674\t4.462516251\t4.472209609\t4.259480191\t4.392390039\t4.395272253\t4.305664387\t4.179207569\t4.396834579\t4.31087313\t4.419271137\t4.039056214\t4.393125083\t4.675851363\t4.364602525\t4.466913655\t4.481694872\t4.318407645\t4.289313676\t4.446749448\t4.571755159\t4.580876703\t4.472186105\t4.571326085\t4.256571368\t4.39667478\t4.528005839\t4.541201304\t4.406940498\t4.545197346\t4.391907474\t4.344684431\t4.477778512\t4.450207826\t4.417370227\t4.386250441\t4.085408476\t4.379901509\t4.215423793\t4.406536979\t4.163083399\t3.963043381\t4.187628652\t4.320252412\t4.545904132\t4.157495172\t4.5392129\t4.355912516\t4.32104914\t4.595052116\t4.387708897\t4.434185544\t4.060156974\t4.416837064\t4.417398742\t4.332046944\t4.248920107\t4.318558306\t4.675950075\t4.188599527\t4.654017827\t4.398818689\t4.448725636\t4.565013209\t4.273248747\t4.353604308\t4.056089953\t4.261860182\t4.366973197\t4.451823465\t4.375387491\t4.392784813\t4.187746104\t4.182184758\t4.06300237\t4.433683963\t4.494079796\t4.423765189\t4.646938456\t4.487248568\t4.175523204\t4.322262883\t4.314792833\t4.211783408\t4.348925516\t4.245849039\t4.482311354\t4.365509618\t4.44930672\t4.232880823\t4.441521421\t4.563517091\t4.331946693\t4.200062175\t4.208486129\t4.241824508\t4.445903314\t4.60948463\t4.517829053\t4.578649469\t4.916165933\t4.654804445\t4.551715167\t4.291265754\t4.874321475\t4.400847348\t4.38994431\t4.303778936\t4.373744009\t4.302854884\t4.598405731\t4.568087675\t4.461992655\t4.464836218\t4.625734497\t4.584892798\t4.662890116\t4.339637524\t4.497000889\t3.983841809\t4.283440095\t4.488303133\t4.296996312\t4.19346948\t4.727898398\t4.28073709\t4.513542781\t4.421895016\t4.313514034\t4.453121704\t4.303450906\t4.055802163\t4.602680714\t4.27076319\t4.224132258\t4.276186679\t4.652756637\t4.634338821\t4.47194762\n+Xanthosine\t4.075879575\t4.195761901\t4.12449321\t4.2502583\t4.361708565\t4.199196067\t4.196265732\t4.404987211\t4.41064782\t4.175794892\t4.258855541\t4.172714224\t4.016015657\t4.100203052\t4.384366912\t4.112921255\t4.399534645\t4.332193324\t4.208322622\t4.379464496\t4.265560718\t4.418307991\t4.087210986\t4.354190761\t3.978396839\t4.172345295\t4.106312026\t4.113942504\t4.558528094\t4.405650867\t3.683591924\t4.26118478\t4.282118008\t3.858642232\t4.299616596\t4.314749151\t4.065692925\t4.144560403\t4.103564195\t3.790628566\t4.416095358\t3.700313782\t4.265516105\t4.289286398\t4.302147514\t4.38354181\t4.218737122\t4.241238791\t4.415874314\t4.120532172\t4.291457181\t4.432756525\t4.239834416\t4.385267423\t4.203494903\t4.352140139\t4.353667915\t4.211041989\t4.471329543\t4.407096124\t4.335026554\t4.295258417\t4.360194162\t4.244628342\t4.523107299\t4.680727647\t4.380119407\t4.50434686\t4.101784524\t4.190726746\t4.702793616\t4.283539498\t4.491848445\t4.628062354\t4.405671691\t4.158371484\t4.227722032\t4.320367885\t4.415241512\t4.640270467\t4.21985738\t4.150109329\t4.265318291\t4.540761333\t4.261018241\t4.151723361\t4.259370091\t4.393426673\t4.870015557\t4.19378655\t4.10780659\t4.016284523\t4.107217721\t4.31688128\t4.49131669\t4.562464053\t4.50079102\t4.281917446\t4.487327505\t4.133987874\t4.186924379\t4.447610934\t4.384756495\t4.455984384\t4.431190839\t4.272439619\t4.515910771\t4.35224905\t4.249140203\t4.126305817\t4.025207129\t4.144468584\t4.370255637\t4.480739473\t4.363577911\t4.194958282\t3.950238979\t4.197796158\t4.489707246\t4.395211284\t4.589147194\t4.410919138\t4.26922062\t4.315277915\t4.516084092\t4.26149305\t5.535146698\t4.244361054\t4.422768199\t4.078743662\t4.434466561\t4.090579617\t4.085780689\t4.48828568\t4.610716761\t4.159093884\t4.139057245\t3.674563769\t4.65106654\t4.176384186\t4.301494215\t4.241053606\t3.94529113\t4.123354762\t3.765637618\t4.203290621\t4.40791255\t4.150929571\t4.289863493\t4.178743871\t4.123566885\t4.345336878\t4.279958081\t4.063705348\t4.069319014\t4.200426656\t4.00966354\t4.200744339\t4.061326655\t4.093155495\t4.514761467\t4.227698791\t4.527880359\t4.507718263\t4.375752047\t4.28503905\t4.235141509\t4.534792548\t4.394130646\t4.523847631\t4.352227778\t4.233160334\t4.253659257\t4.031631259\t4.426082168\t4.500371235\t4.186340083\t4.629825565\t4.408696151\t4.3878006\t4.256140724\t4.487781609\t4.222953354\n' |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b runit/sacurine/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/sacurine/sampleMetadata.tsv Sat Aug 06 12:17:12 2016 -0400 |
| b |
| @@ -0,0 +1,184 @@ + age bmi gender +HU_011 29 19.75 M +HU_014 59 22.64 F +HU_015 42 22.72 M +HU_017 41 23.03 M +HU_018 34 20.96 M +HU_019 35 23.41 M +HU_020 59 17.1 M +HU_021 34 23.36 M +HU_022 51 28.23 F +HU_023 51 29.55 M +HU_024 57 29.86 M +HU_025 53 21.6 M +HU_026 34 23.46 F +HU_027 37 24.82 M +HU_028 41 23.92 F +HU_029 37 27.78 M +HU_030 49 25.88 M +HU_031 25 20.76 M +HU_032 38 24.09 F +HU_033 44 18.36 F +HU_034 52 23.37 M +HU_035 37 20.7 F +HU_036 47 29.51 M +HU_037 35 25.62 M +HU_038 52 22.72 M +HU_039 45 24.9 M +HU_040 24 26.54 M +HU_041 28 23.67 M +HU_042 36 19.75 M +HU_043 42 29.04 M +HU_044 57 25.46 F +HU_045 46 20.81 F +HU_046 35 24.84 M +HU_047 43 25 F +HU_048 39 19.49 F +HU_049 50 27.85 M +HU_050 30 24.21 M +HU_051 24 23.23 F +HU_052 51 20.06 F +HU_053 49 25.88 M +HU_054 29 20.76 M +HU_055 58 24.89 F +HU_056 41 21.15 M +HU_057 57 27.16 M +HU_058 45 26.7 M +HU_060 55 28.72 F +HU_061 44 25.35 F +HU_062 34 22.22 M +HU_063 35 21.01 F +HU_064 32 21.94 F +HU_065 54 21.87 M +HU_066 25 22.53 F +HU_067 40 19.31 F +HU_068 37 27.22 F +HU_069 39 24.38 M +HU_070 58 18.71 M +HU_072 47 27.13 M +HU_073 35 25.38 M +HU_074 42 20.94 F +HU_075 38 21.05 M +HU_076 47 26.7 M +HU_077 27 21.15 M +HU_078 46 25.18 M +HU_079 47 23.55 M +HU_080 21 19.72 F +HU_081 25 17.84 F +HU_082 49 23.15 M +HU_083 50 29.76 M +HU_084 62 23.8 F +HU_085 23 22.86 M +HU_086 33 23.51 M +HU_087 38 23.8 F +HU_088 50 21.78 F +HU_089 31 23.7 M +HU_090 46 19.79 M +HU_091 61 26.12 M +HU_092 40 21.83 M +HU_093 53 21.71 M +HU_094 32 23.29 M +HU_095 27 27.33 M +HU_097 50 26.78 M +HU_098 46 20.45 M +HU_099 23 21.3 M +HU_100 47 21.22 F +HU_101 39 23.7 M +HU_102 59 24.03 F +HU_103 49 26.79 M +HU_105 47 22.96 M +HU_106 42 27.34 M +HU_107 46 24.22 M +HU_108 25 23.81 M +HU_109 32 22.68 M +HU_110 50 20.9 F +HU_112 55 25.36 M +HU_113 44 23.05 M +HU_114 58 29.38 M +HU_115 46 27.24 F +HU_116 28 20.96 F +HU_117 24 22.86 M +HU_118 30 21.64 F +HU_119 50 24.44 F +HU_120 32 23.88 F +HU_121 26 20.57 M +HU_122 48 23.03 M +HU_123 49 24.39 M +HU_124 34 22.22 M +HU_125 58 25.47 M +HU_126 45 24.7 M +HU_127 45 25.62 M +HU_129 47 29.32 M +HU_130 33 26.06 M +HU_131 42 23.12 M +HU_132 38 26.67 F +HU_133 53 25.43 M +HU_134 48 22.89 M +HU_135 31 24.93 M +HU_136 52 20.81 F +HU_137 28 22.22 M +HU_138 42 21.88 M +HU_139 47 23.03 M +HU_140 49 26.59 M +HU_142 25 20.98 M +HU_143 52 23.15 F +HU_144 38 29.54 M +HU_145 27 29.09 M +HU_146 42 24.21 M +HU_147 60 31.74 M +HU_148 55 30.48 F +HU_149 35 19.49 F +HU_150 49 27.24 F +HU_152 26 17.58 F +HU_154 35 27.71 F +HU_155 48 20.45 F +HU_156 36 16.85 F +HU_157 43 21.95 F +HU_158 50 25.48 F +HU_159 37 21.72 F +HU_160 31 24.17 F +HU_162 50 29.03 F +HU_163 49 23.15 F +HU_164 45 25.63 F +HU_166 40 19.72 F +HU_167 55 20.57 F +HU_168 37 20.76 F +HU_169 53 19.14 F +HU_170 50 24.61 F +HU_171 29 21.37 F +HU_172 55 21.36 F +HU_173 55 20.28 F +HU_174 42 31.64 F +HU_175 35 21.26 F +HU_177 59 28.58 F +HU_179 33 26.57 F +HU_180 53 23.74 F +HU_181 49 22.46 F +HU_182 43 23.74 F +HU_183 46 19.13 F +HU_184 37 25.33 F +HU_185 42 21.09 F +HU_186 44 22.1 F +HU_187 21 19.95 F +HU_188 22 24.22 F +HU_189 39 19.43 F +HU_190 28 25.93 M +HU_191 36 26.12 M +HU_192 31 24.22 M +HU_193 35 21.78 F +HU_194 40 28.04 F +HU_195 26 18.42 F +HU_196 27 21.1 F +HU_197 26 20.72 M +HU_198 35 22.98 M +HU_199 33 21.04 M +HU_200 46 23.89 M +HU_201 34 20.24 M +HU_202 42 28.06 M +HU_203 25 19.95 F +HU_204 31 29.06 M +HU_205 33 28.37 M +HU_206 45 22.15 F +HU_207 33 19.47 F +HU_208 27 18.61 F +HU_209 17.5 21.48 F |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b runit/sacurine/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/sacurine/variableMetadata.tsv Sat Aug 06 12:17:12 2016 -0400 |
| b |
| @@ -0,0 +1,110 @@ + msiLevel hmdb chemicalClass +(2-methoxyethoxy)propanoic acid isomer 2 Organi +(gamma)Glu-Leu/Ile 2 AA-pep +1-Methyluric acid 1 HMDB03099 AroHeP:Xenobi +1-Methylxanthine 1 HMDB10738 AroHeP +1,3-Dimethyluric acid 1 HMDB01857 AroHeP +1,7-Dimethyluric acid 1 HMDB11103 AroHeP +2-acetamido-4-methylphenyl acetate 2 AroHoM +2-Aminoadipic acid 1 HMDB00510 AA-pep +2-Hydroxybenzyl alcohol 1 HMDB59709 AroHoM +2-Isopropylmalic acid 1 HMDB00402 Organi +2-Methylhippuric acid 1 HMDB11723 AA-pep:AcyGly +2,2-Dimethylglutaric acid 1 Lipids +3-Hydroxybenzyl alcohol 1 HMDB59712 AroHoM +3-Hydroxyphenylacetic acid 1 HMDB00440 AroHoM +3-Indole carboxylic acid glucuronide 2 HMDB13189 Carboh +3-Methyl-2-oxovaleric acid 1 HMDB00491 Lipids +3-Methylcrotonylglycine 1 HMDB00459 AA-pep:AcyGly +3,3-Dimethylglutaric acid 1 HMDB02441 Lipids +3,4-Dihydroxybenzeneacetic acid 1 HMDB01336 AroHoM +3,5-dihydroxybenzoic acid/3,4-dihydroxybenzoic acid 2 AroHoM +3,7-Dimethyluric acid 1 HMDB01982 AroHeP +4-Acetamidobutanoic acid isomer 2 2 Lipids +4-Acetamidobutanoic acid isomer 3 2 Lipids +4-Hydroxybenzoic acid 1 HMDB00500 AroHoM +4-Methylhippuric acid/3-Methylhippuric acid 1 AA-pep:AcyGly +5-Hydroxyindoleacetic acid 1 HMDB00763 AroHeP +5-Sulfosalicylic acid 1 HMDB11725 AroHoM +6-(2-hydroxyethoxy)-6-oxohexanoic acid 2 Organi +6-(carboxymethoxy)-hexanoic acid 2 Organi +9-Methylxanthine 2 HMDB59716 AroHeP +Acetaminophen glucuronide 1 HMDB10316 Carboh +Acetylphenylalanine 1 HMDB00512 AA-pep +alpha-N-Phenylacetyl-glutamine 1 HMDB06344 AA-pep +Aminosalicyluric acid 2 AA-pep:AcyGly +Asp-Leu/Ile isomer 1 2 AA-pep +Asp-Leu/Ile isomer 2 2 AA-pep +Aspartic acid 1 HMDB00191 AA-pep +Azelaic acid 1 HMDB00784 Organi +Benzoic acid isomer 2 AroHoM +Chenodeoxycholic acid isomer 2 Lipids:Steroi +Cinnamoylglycine 1 HMDB11621 AA-pep:AcyGly +Citric acid 1 HMDB00094 Organi +Dehydroepiandrosterone 3-glucuronide 1 HMDB10348 Lipids:Steroi +Dehydroepiandrosterone sulfate 1 HMDB01032 Lipids:Steroi +Deoxyhexose 1 HMDB00849 Carboh +Dimethylguanosine 2 HMDB04824 Nucleo +FMNH2 2 HMDB01142 AroHeP +Fumaric acid 1 HMDB00134 Lipids +Gentisic acid 1 HMDB00152 AroHoM +Glu-Val 2 HMDB59717 AA-pep +Gluconic acid and/or isomers 2 Carboh +Glucuronic acid and/or isomers 2 Carboh +Glyceric acid 1 HMDB00139 Carboh +Glycocholic acid isomer 2 2 Lipids:Steroi +Glycocholic acid isomer 3 2 Lipids:Steroi +Heptylmalonic acid 2 HMDB59719 Lipids +Hexanoylglycine 1 HMDB00701 AA-pep:AcyGly +Hippuric acid 1 HMDB00714 AA-pep:AcyGly +Hydroxybenzyl alcohol isomer 2 AroHeM +Hydroxyphenyllactic acid 1 HMDB00755 AroHoM +Hydroxysuberic acid isomer 1 2 Organi +Hydroxysuberic acid isomer 2 2 Organi +Isovalerylalanine isomer 2 AA-pep +Ketoleucine 1 HMDB00695 Lipids +Kynurenic acid 1 HMDB00715 AA-pep +Malic acid 1 HMDB00156 Organi +Methoxysalicylic acid isomer 2 AroHoM +Methyl (hydroxymethyl)pyrrolidine-carboxylate/Methyl (hydroxy)piperidine-carboxylate 2 AA-pep +Methylinosine 2 Nucleo +Mevalonic acid isomer 1 2 Organi +Monoethyl phthalate 2 HMDB02120 AroHoM:Xenobi +N-Acetyl-aspartic acid 1 HMDB00812 AA-pep +N-Acetylisoleucine 1 AA-pep +N-Acetylleucine 1 HMDB11756 AA-pep +N-Acetyltryptophan 1 HMDB13713 AA-pep +N-Acetyltryptophan isomer 3 2 AA-pep +N2-Acetylaminoadipic acid 2 AA-pep +N4-Acetylcytidine 1 HMDB05923 Nucleo +Nicotinuric acid isomer 2 AA-pep +Ortho-Hydroxyphenylacetic acid 1 HMDB00669 AroHoM +Oxoglutaric acid 2 HMDB00208 Organi +p-Anisic acid 1 HMDB01101 AroHoM +p-Hydroxyhippuric acid 2 HMDB13678 AA-pep:AcyGly +p-Hydroxymandelic acid 1 HMDB00822 AroHoM +p-Hydroxyphenylacetic acid 1 HMDB00020 AroHoM +Pantothenic acid 1 HMDB00210 AliAcy +Pentose 2 Carboh +Phe-Tyr-Asp (and isomers) 2 AA-pep +Porphobilinogen 1 HMDB00245 Organi +Pyridoxic acid isomer 1 2 AroHeM +Pyridylacetylglycine 2 HMDB59723 AA-pep:AcyGly:Xenobi +Pyrocatechol sulfate 2 HMDB59724 AroHoM +Pyroglutamic acid 1 HMDB00267 AliHeM +Pyrroledicarboxylic acid 2 AroHeM +Pyruvic acid 1 HMDB00243 Organi +Quinic acid 1 HMDB03072 AliHoM +Salicylic acid 1 HMDB01895 AroHoM:Xenobi +Sebacic acid 1 HMDB00792 Organi +Suberic acid 1 HMDB00893 Organi +Sulfosalicylic acid isomer 2 AroHoM +Taurine 1 HMDB00251 Organi +Testosterone glucuronide 2 HMDB03193 Lipids:Steroi +Tetrahydrohippuric acid 2 AA-pep:AcyGly +Threo-3-Phenylserine 1 HMDB02184 AA-pep +Threonic acid/Erythronic acid 2 Carboh +Tryptophan 1 HMDB00929 AA-pep +Valerylglycine isomer 1 2 AA-pep:AcyGly +Valerylglycine isomer 2 2 AA-pep:AcyGly +Xanthosine 1 HMDB00299 Nucleo |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b tests/biosigner_tests.R --- a/tests/biosigner_tests.R Sat Jul 30 12:21:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,264 +0,0 @@\n-library(RUnit)\n-\n-wrapperF <- function(argVc) {\n-\n-\n-#### Start_of_testing_code <- function() {}\n-\n-\n-##------------------------------\n-## Initializing\n-##------------------------------\n-\n-## options\n-##--------\n-\n-strAsFacL <- options()$stringsAsFactors\n-options(stringsAsFactors = FALSE)\n-\n-## libraries\n-##----------\n-\n-suppressMessages(library(biosigner))\n-\n-if(packageVersion("biosigner") < "1.0.0")\n- stop("Please use \'biosigner\' versions of 1.0.0 and above")\n-if(packageVersion("ropls") < "1.4.0")\n- stop("Please use \'ropls\' versions of 1.4.0 and above")\n-\n-## constants\n-##----------\n-\n-modNamC <- "Biosigner" ## module name\n-\n-topEnvC <- environment()\n-flgC <- "\\n"\n-\n-## functions\n-##----------\n-\n-flgF <- function(tesC,\n- envC = topEnvC,\n- txtC = NA) { ## management of warning and error messages\n-\n- tesL <- eval(parse(text = tesC), envir = envC)\n-\n- if(!tesL) {\n-\n- sink(NULL)\n- stpTxtC <- ifelse(is.na(txtC),\n- paste0(tesC, " is FALSE"),\n- txtC)\n-\n- stop(stpTxtC,\n- call. = FALSE)\n-\n- }\n-\n-} ## flgF\n-\n-\n-## log file\n-##---------\n-\n-sink(argVc["information"])\n-\n-cat("\\nStart of the \'", modNamC, "\' Galaxy module call: ",\n- format(Sys.time(), "%a %d %b %Y %X"), "\\n", sep="")\n-\n-\n-## arguments\n-##----------\n-\n-xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],\n- check.names = FALSE,\n- header = TRUE,\n- row.names = 1,\n- sep = "\\t")))\n-\n-samDF <- read.table(argVc["sampleMetadata_in"],\n- check.names = FALSE,\n- header = TRUE,\n- row.names = 1,\n- sep = "\\t")\n-flgF("identical(rownames(xMN), rownames(samDF))", txtC = "Sample names (or number) in the data matrix (first row) and sample metadata (first column) are not identical; use the \'Check Format\' module in the \'Quality Control\' section")\n-\n-varDF <- read.table(argVc["variableMetadata_in"],\n- check.names = FALSE,\n- header = TRUE,\n- row.names = 1,\n- sep = "\\t")\n-flgF("identical(colnames(xMN), rownames(varDF))", txtC = "Variable names (or number) in the data matrix (first column) and sample metadata (first column) are not identical; use the \'Check Format\' module in the \'Quality Control\' section")\n-\n-flgF("argVc[\'respC\'] %in% colnames(samDF)",\n- txtC = paste0("Class argument (", argVc[\'respC\'], ") must be either none or one of the column names (first row) of your sample metadata"))\n-respVc <- samDF[, argVc["respC"]]\n-flgF("mode(respVc) == \'character\'",\n- txtC = paste0("\'", argVc[\'respC\'], "\' column of sampleMetadata does not contain only characters"))\n-respFc <- factor(respVc)\n-flgF("length(levels(respFc)) == 2",\n- txtC = paste0("\'", argVc[\'respC\'], "\' column of sampleMetadata does not contain only 2 types of characters (e.g., \'case\' and \'control\')"))\n-tierMaxC <- ifelse("tierC" %in% names(argVc), argVc["tierC"], "S")\n-pvalN <- ifelse("pvalN" %in% names(argVc), as.numeric(argVc["pvalN"]), 0.05)\n-\n-\n-##------------------------------\n-## Computation and plot\n-##------------------------------\n-\n-\n-sink()\n-\n-optWrnN <- options()$warn\n-options(warn = -1)\n-\n-if("seedI" %in% names(argVc) && argVc["seedI"] != "0")\n- set.seed(as.integer(argVc["seedI"]))\n-\n-bsnLs <- biosign(x = xMN,\n- y = respFc,\n- methodVc = ifelse("methodC" %in% names(argVc), argVc["methodC"], "all"),\n- bootI = ifelse("bootI" %in% names(argVc), as.numeric(argVc["bootI"]), 50),\n- pvalN = pvalN,\n- printL = FALSE,\n- plotL = FALSE,\n- .sinkC = argVc["information"])\n-\n-if("seedI" %in% names(argVc) && argVc["seedI"] != "0")\n- set.seed(NULL)\n-\n-tierMC <- bsnLs@tierMC\n-\n-if(!is.null(tierMC)) {\n- '..b'argVc["figure_tier"])\n- plot(1, bty = "n", type = "n",\n- xaxt = "n", yaxt = "n", xlab = "", ylab = "")\n- text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),\n- labels = "No significant variable to display")\n- dev.off()\n- pdf(argVc["figure_boxplot"])\n- plot(1, bty = "n", type = "n",\n- xaxt = "n", yaxt = "n", xlab = "", ylab = "")\n- text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),\n- labels = "No significant variable to display")\n- dev.off()\n-}\n-\n-\n-options(warn = optWrnN)\n-\n-\n-##------------------------------\n-## Print\n-##------------------------------\n-\n-sink(argVc["information"], append = TRUE)\n-\n-tierFullVc <- c("S", LETTERS[1:5])\n-tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]\n-\n-if(sum(tierMC %in% tierVc)) {\n- cat("\\nSignificant features from \'", paste(tierVc, collapse = "\', \'"), "\' tiers:\\n", sep = "")\n- print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,\n- drop = FALSE])\n- cat("\\nAccuracy:\\n")\n- print(round(getAccuracyMN(bsnLs), 3))\n-} else\n- cat("\\nNo significant variable found for any classifier\\n")\n-\n-\n-##------------------------------\n-## Ending\n-##------------------------------\n-\n-## Saving\n-##-------\n-\n-if(!is.null(tierMC)) {\n- tierDF <- data.frame(tier = sapply(rownames(varDF),\n- function(varC) {\n- varTirVc <- tierMC[varC, ]\n- varTirVc <- names(varTirVc)[varTirVc %in% tierVc]\n- paste(varTirVc, collapse = "|")\n- }),\n- stringsAsFactors = FALSE)\n- colnames(tierDF) <- paste(argVc["respC"],\n- colnames(tierDF),\n- paste(tierVc, collapse = ""),\n- sep = "_")\n- varDF <- cbind.data.frame(varDF, tierDF)\n-}\n-\n-## variableMetadata\n-\n-varDF <- cbind.data.frame(variableMetadata = rownames(varDF),\n- varDF)\n-write.table(varDF,\n- file = argVc["variableMetadata_out"],\n- quote = FALSE,\n- row.names = FALSE,\n- sep = "\\t")\n-\n-\n-## Closing\n-##--------\n-\n-cat("\\nEnd of \'", modNamC, "\' Galaxy module call: ",\n- as.character(Sys.time()), "\\n", sep = "")\n-\n-sink()\n-\n-options(stringsAsFactors = strAsFacL)\n-\n-\n-#### End_of_testing_code <- function() {}\n-\n-\n- return(list(bsnLs = bsnLs))\n-\n-\n- rm(list = ls())\n-\n-\n-}\n-\n-\n-exaDirOutC <- "output"\n-if(!file.exists(exaDirOutC))\n- stop("Please create an \'output\' subfolder into the (current) \'tests\' folder")\n-\n-tesArgLs <- list(sacurine_all = c(respC = "gender",\n- methodC = "all",\n- bootI = "5",\n- pvalN = "0.05",\n- seedI = "123",\n- .chkC = "checkEqualsNumeric(getAccuracyMN(outLs[[\'bsnLs\']])[\'AS\', \'randomforest\'], 0.8534348, tolerance = 1e-7)"))\n-\n-for(tesC in names(tesArgLs))\n- tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],\n- dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),\n- sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"),\n- variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"),\n- variableMetadata_out = file.path(exaDirOutC, "variableMetadata.tsv"),\n- figure_tier = file.path(exaDirOutC, "figure-tier.pdf"),\n- figure_boxplot = file.path(exaDirOutC, "figure-boxplot.pdf"),\n- information = file.path(exaDirOutC, "information.txt"))\n-\n-for(tesC in names(tesArgLs)) {\n- print(tesC)\n- outLs <- wrapperF(tesArgLs[[tesC]])\n- if(".chkC" %in% names(tesArgLs[[tesC]]))\n- stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))\n-}\n-\n-message("Checks successfully completed")\n' |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b tests/sacurine/dataMatrix.tsv --- a/tests/sacurine/dataMatrix.tsv Sat Jul 30 12:21:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,110 +0,0 @@\n-\tHU_011\tHU_014\tHU_015\tHU_017\tHU_018\tHU_019\tHU_020\tHU_021\tHU_022\tHU_023\tHU_024\tHU_025\tHU_026\tHU_027\tHU_028\tHU_029\tHU_030\tHU_031\tHU_032\tHU_033\tHU_034\tHU_035\tHU_036\tHU_037\tHU_038\tHU_039\tHU_040\tHU_041\tHU_042\tHU_043\tHU_044\tHU_045\tHU_046\tHU_047\tHU_048\tHU_049\tHU_050\tHU_051\tHU_052\tHU_053\tHU_054\tHU_055\tHU_056\tHU_057\tHU_058\tHU_060\tHU_061\tHU_062\tHU_063\tHU_064\tHU_065\tHU_066\tHU_067\tHU_068\tHU_069\tHU_070\tHU_072\tHU_073\tHU_074\tHU_075\tHU_076\tHU_077\tHU_078\tHU_079\tHU_080\tHU_081\tHU_082\tHU_083\tHU_084\tHU_085\tHU_086\tHU_087\tHU_088\tHU_089\tHU_090\tHU_091\tHU_092\tHU_093\tHU_094\tHU_095\tHU_097\tHU_098\tHU_099\tHU_100\tHU_101\tHU_102\tHU_103\tHU_105\tHU_106\tHU_107\tHU_108\tHU_109\tHU_110\tHU_112\tHU_113\tHU_114\tHU_115\tHU_116\tHU_117\tHU_118\tHU_119\tHU_120\tHU_121\tHU_122\tHU_123\tHU_124\tHU_125\tHU_126\tHU_127\tHU_129\tHU_130\tHU_131\tHU_132\tHU_133\tHU_134\tHU_135\tHU_136\tHU_137\tHU_138\tHU_139\tHU_140\tHU_142\tHU_143\tHU_144\tHU_145\tHU_146\tHU_147\tHU_148\tHU_149\tHU_150\tHU_152\tHU_154\tHU_155\tHU_156\tHU_157\tHU_158\tHU_159\tHU_160\tHU_162\tHU_163\tHU_164\tHU_166\tHU_167\tHU_168\tHU_169\tHU_170\tHU_171\tHU_172\tHU_173\tHU_174\tHU_175\tHU_177\tHU_179\tHU_180\tHU_181\tHU_182\tHU_183\tHU_184\tHU_185\tHU_186\tHU_187\tHU_188\tHU_189\tHU_190\tHU_191\tHU_192\tHU_193\tHU_194\tHU_195\tHU_196\tHU_197\tHU_198\tHU_199\tHU_200\tHU_201\tHU_202\tHU_203\tHU_204\tHU_205\tHU_206\tHU_207\tHU_208\tHU_209\n-(2-methoxyethoxy)propanoic acid isomer\t3.019766011\t3.81433889\t3.51969148\t2.56218265\t3.781921607\t4.161073524\t3.199174022\t3.378109516\t3.26452758\t3.787490017\t5.36371403\t3.202345706\t3.980345369\t3.020293232\t5.083462878\t3.388718935\t3.445549982\t1.27650453\t3.738547491\t1.253594534\t3.232847813\t4.559559002\t4.075948481\t2.570748216\t4.117811641\t5.038208548\t4.394350472\t3.665845239\t3.42296993\t3.74546685\t3.110957103\t4.252742233\t4.296284046\t2.995377877\t3.389971588\t5.349114655\t5.813374487\t4.304743135\t1.435768568\t5.369591232\t3.809431106\t3.0110849\t1.321147859\t3.401176446\t3.506978677\t5.24237122\t3.416889621\t3.415584225\t3.887678774\t3.555974489\t3.710985751\t4.232236312\t3.803661779\t4.379572071\t3.938310455\t1.376325833\t3.390271579\t5.215817481\t4.351838419\t3.714724817\t3.529736242\t3.862848205\t3.383427403\t3.661146136\t4.112188079\t4.249731699\t4.765467314\t3.51532253\t4.155850086\t4.045784307\t4.222815204\t4.168351191\t4.21782555\t3.612098315\t3.073157836\t4.235420499\t3.820636952\t2.797679916\t3.136688731\t3.665614604\t4.154569098\t4.299336631\t3.559309507\t2.996742676\t3.480758857\t4.034741661\t3.856739467\t2.852684744\t3.651373844\t3.759574346\t3.95537384\t2.849099312\t3.398179811\t3.984515153\t3.597414226\t3.290898684\t4.179746804\t4.943696911\t1.555387577\t3.60408986\t1.301552667\t3.640714337\t3.9838544\t3.827632696\t4.969533288\t3.504223072\t2.927962237\t4.011233932\t3.846480069\t3.945182011\t3.444671991\t3.617341684\t4.433665852\t3.758001601\t3.117921102\t3.604887175\t3.827127682\t1.270341972\t4.661967452\t3.058563173\t4.718036674\t3.77969937\t4.41111843\t3.735829951\t3.867366105\t3.377810236\t4.174630078\t4.051745447\t4.354188592\t3.522532268\t3.278058138\t3.375142493\t4.201257373\t3.531025311\t4.104608416\t3.308431289\t3.645655442\t5.077657223\t1.307713092\t4.169713633\t3.588749002\t3.785980907\t3.237049946\t4.089354447\t3.881406873\t3.732585337\t4.054073292\t4.137363308\t4.493012079\t4.930648019\t3.399303204\t3.372649157\t3.808510752\t3.912572116\t4.87526109\t3.423336878\t4.817034951\t3.574103433\t3.392706279\t3.640266302\t3.918027353\t2.984720403\t4.912949546\t3.391126097\t3.496992454\t4.454290676\t3.679442656\t4.082141098\t3.901748493\t4.459292151\t3.658028576\t3.61865837\t1.347192548\t3.156817506\t4.088827883\t3.68482537\t3.739437875\t3.62621039\t3.861325975\t1.321648909\t4.186987285\t3.748127215\t4.208859398\n-(gamma)Glu-Leu/Ile\t3.888479324\t4.277148905\t4.195649235\t4.323759965\t4.629328558\t4.412266289\t4.175236737\t4.635271487\t3.847144646\t3.871586241\t4.417740636\t4.328564559\t4.02953783\t4.152376569\t4.292682632\t4.531347748\t4.453076004\t4.6291358\t4.113221891\t4.150947299\t4.124072576\t3.901047415\t4.024811926\t4.181515516\t4.181368916\t3.876389846\t4.704956128\t4.21159738\t4.336920642\t4.38187405\t3.899552672\t4.061643136\t4.379398702\t3.828154643\t4.197557784\t4.015019635\t4.401325613\t3.802961064\t4.191430823\t4.'..b'049\t4.330382886\t4.100121431\t4.320047243\t4.239744811\t4.150606181\t4.124659917\t4.375400222\t4.251030211\t3.777775091\t4.361487807\t4.082842319\t4.083917302\t4.325269835\t4.010354674\t4.462516251\t4.472209609\t4.259480191\t4.392390039\t4.395272253\t4.305664387\t4.179207569\t4.396834579\t4.31087313\t4.419271137\t4.039056214\t4.393125083\t4.675851363\t4.364602525\t4.466913655\t4.481694872\t4.318407645\t4.289313676\t4.446749448\t4.571755159\t4.580876703\t4.472186105\t4.571326085\t4.256571368\t4.39667478\t4.528005839\t4.541201304\t4.406940498\t4.545197346\t4.391907474\t4.344684431\t4.477778512\t4.450207826\t4.417370227\t4.386250441\t4.085408476\t4.379901509\t4.215423793\t4.406536979\t4.163083399\t3.963043381\t4.187628652\t4.320252412\t4.545904132\t4.157495172\t4.5392129\t4.355912516\t4.32104914\t4.595052116\t4.387708897\t4.434185544\t4.060156974\t4.416837064\t4.417398742\t4.332046944\t4.248920107\t4.318558306\t4.675950075\t4.188599527\t4.654017827\t4.398818689\t4.448725636\t4.565013209\t4.273248747\t4.353604308\t4.056089953\t4.261860182\t4.366973197\t4.451823465\t4.375387491\t4.392784813\t4.187746104\t4.182184758\t4.06300237\t4.433683963\t4.494079796\t4.423765189\t4.646938456\t4.487248568\t4.175523204\t4.322262883\t4.314792833\t4.211783408\t4.348925516\t4.245849039\t4.482311354\t4.365509618\t4.44930672\t4.232880823\t4.441521421\t4.563517091\t4.331946693\t4.200062175\t4.208486129\t4.241824508\t4.445903314\t4.60948463\t4.517829053\t4.578649469\t4.916165933\t4.654804445\t4.551715167\t4.291265754\t4.874321475\t4.400847348\t4.38994431\t4.303778936\t4.373744009\t4.302854884\t4.598405731\t4.568087675\t4.461992655\t4.464836218\t4.625734497\t4.584892798\t4.662890116\t4.339637524\t4.497000889\t3.983841809\t4.283440095\t4.488303133\t4.296996312\t4.19346948\t4.727898398\t4.28073709\t4.513542781\t4.421895016\t4.313514034\t4.453121704\t4.303450906\t4.055802163\t4.602680714\t4.27076319\t4.224132258\t4.276186679\t4.652756637\t4.634338821\t4.47194762\n-Xanthosine\t4.075879575\t4.195761901\t4.12449321\t4.2502583\t4.361708565\t4.199196067\t4.196265732\t4.404987211\t4.41064782\t4.175794892\t4.258855541\t4.172714224\t4.016015657\t4.100203052\t4.384366912\t4.112921255\t4.399534645\t4.332193324\t4.208322622\t4.379464496\t4.265560718\t4.418307991\t4.087210986\t4.354190761\t3.978396839\t4.172345295\t4.106312026\t4.113942504\t4.558528094\t4.405650867\t3.683591924\t4.26118478\t4.282118008\t3.858642232\t4.299616596\t4.314749151\t4.065692925\t4.144560403\t4.103564195\t3.790628566\t4.416095358\t3.700313782\t4.265516105\t4.289286398\t4.302147514\t4.38354181\t4.218737122\t4.241238791\t4.415874314\t4.120532172\t4.291457181\t4.432756525\t4.239834416\t4.385267423\t4.203494903\t4.352140139\t4.353667915\t4.211041989\t4.471329543\t4.407096124\t4.335026554\t4.295258417\t4.360194162\t4.244628342\t4.523107299\t4.680727647\t4.380119407\t4.50434686\t4.101784524\t4.190726746\t4.702793616\t4.283539498\t4.491848445\t4.628062354\t4.405671691\t4.158371484\t4.227722032\t4.320367885\t4.415241512\t4.640270467\t4.21985738\t4.150109329\t4.265318291\t4.540761333\t4.261018241\t4.151723361\t4.259370091\t4.393426673\t4.870015557\t4.19378655\t4.10780659\t4.016284523\t4.107217721\t4.31688128\t4.49131669\t4.562464053\t4.50079102\t4.281917446\t4.487327505\t4.133987874\t4.186924379\t4.447610934\t4.384756495\t4.455984384\t4.431190839\t4.272439619\t4.515910771\t4.35224905\t4.249140203\t4.126305817\t4.025207129\t4.144468584\t4.370255637\t4.480739473\t4.363577911\t4.194958282\t3.950238979\t4.197796158\t4.489707246\t4.395211284\t4.589147194\t4.410919138\t4.26922062\t4.315277915\t4.516084092\t4.26149305\t5.535146698\t4.244361054\t4.422768199\t4.078743662\t4.434466561\t4.090579617\t4.085780689\t4.48828568\t4.610716761\t4.159093884\t4.139057245\t3.674563769\t4.65106654\t4.176384186\t4.301494215\t4.241053606\t3.94529113\t4.123354762\t3.765637618\t4.203290621\t4.40791255\t4.150929571\t4.289863493\t4.178743871\t4.123566885\t4.345336878\t4.279958081\t4.063705348\t4.069319014\t4.200426656\t4.00966354\t4.200744339\t4.061326655\t4.093155495\t4.514761467\t4.227698791\t4.527880359\t4.507718263\t4.375752047\t4.28503905\t4.235141509\t4.534792548\t4.394130646\t4.523847631\t4.352227778\t4.233160334\t4.253659257\t4.031631259\t4.426082168\t4.500371235\t4.186340083\t4.629825565\t4.408696151\t4.3878006\t4.256140724\t4.487781609\t4.222953354\n' |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b tests/sacurine/sampleMetadata.tsv --- a/tests/sacurine/sampleMetadata.tsv Sat Jul 30 12:21:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,184 +0,0 @@ - age bmi gender -HU_011 29 19.75 M -HU_014 59 22.64 F -HU_015 42 22.72 M -HU_017 41 23.03 M -HU_018 34 20.96 M -HU_019 35 23.41 M -HU_020 59 17.1 M -HU_021 34 23.36 M -HU_022 51 28.23 F -HU_023 51 29.55 M -HU_024 57 29.86 M -HU_025 53 21.6 M -HU_026 34 23.46 F -HU_027 37 24.82 M -HU_028 41 23.92 F -HU_029 37 27.78 M -HU_030 49 25.88 M -HU_031 25 20.76 M -HU_032 38 24.09 F -HU_033 44 18.36 F -HU_034 52 23.37 M -HU_035 37 20.7 F -HU_036 47 29.51 M -HU_037 35 25.62 M -HU_038 52 22.72 M -HU_039 45 24.9 M -HU_040 24 26.54 M -HU_041 28 23.67 M -HU_042 36 19.75 M -HU_043 42 29.04 M -HU_044 57 25.46 F -HU_045 46 20.81 F -HU_046 35 24.84 M -HU_047 43 25 F -HU_048 39 19.49 F -HU_049 50 27.85 M -HU_050 30 24.21 M -HU_051 24 23.23 F -HU_052 51 20.06 F -HU_053 49 25.88 M -HU_054 29 20.76 M -HU_055 58 24.89 F -HU_056 41 21.15 M -HU_057 57 27.16 M -HU_058 45 26.7 M -HU_060 55 28.72 F -HU_061 44 25.35 F -HU_062 34 22.22 M -HU_063 35 21.01 F -HU_064 32 21.94 F -HU_065 54 21.87 M -HU_066 25 22.53 F -HU_067 40 19.31 F -HU_068 37 27.22 F -HU_069 39 24.38 M -HU_070 58 18.71 M -HU_072 47 27.13 M -HU_073 35 25.38 M -HU_074 42 20.94 F -HU_075 38 21.05 M -HU_076 47 26.7 M -HU_077 27 21.15 M -HU_078 46 25.18 M -HU_079 47 23.55 M -HU_080 21 19.72 F -HU_081 25 17.84 F -HU_082 49 23.15 M -HU_083 50 29.76 M -HU_084 62 23.8 F -HU_085 23 22.86 M -HU_086 33 23.51 M -HU_087 38 23.8 F -HU_088 50 21.78 F -HU_089 31 23.7 M -HU_090 46 19.79 M -HU_091 61 26.12 M -HU_092 40 21.83 M -HU_093 53 21.71 M -HU_094 32 23.29 M -HU_095 27 27.33 M -HU_097 50 26.78 M -HU_098 46 20.45 M -HU_099 23 21.3 M -HU_100 47 21.22 F -HU_101 39 23.7 M -HU_102 59 24.03 F -HU_103 49 26.79 M -HU_105 47 22.96 M -HU_106 42 27.34 M -HU_107 46 24.22 M -HU_108 25 23.81 M -HU_109 32 22.68 M -HU_110 50 20.9 F -HU_112 55 25.36 M -HU_113 44 23.05 M -HU_114 58 29.38 M -HU_115 46 27.24 F -HU_116 28 20.96 F -HU_117 24 22.86 M -HU_118 30 21.64 F -HU_119 50 24.44 F -HU_120 32 23.88 F -HU_121 26 20.57 M -HU_122 48 23.03 M -HU_123 49 24.39 M -HU_124 34 22.22 M -HU_125 58 25.47 M -HU_126 45 24.7 M -HU_127 45 25.62 M -HU_129 47 29.32 M -HU_130 33 26.06 M -HU_131 42 23.12 M -HU_132 38 26.67 F -HU_133 53 25.43 M -HU_134 48 22.89 M -HU_135 31 24.93 M -HU_136 52 20.81 F -HU_137 28 22.22 M -HU_138 42 21.88 M -HU_139 47 23.03 M -HU_140 49 26.59 M -HU_142 25 20.98 M -HU_143 52 23.15 F -HU_144 38 29.54 M -HU_145 27 29.09 M -HU_146 42 24.21 M -HU_147 60 31.74 M -HU_148 55 30.48 F -HU_149 35 19.49 F -HU_150 49 27.24 F -HU_152 26 17.58 F -HU_154 35 27.71 F -HU_155 48 20.45 F -HU_156 36 16.85 F -HU_157 43 21.95 F -HU_158 50 25.48 F -HU_159 37 21.72 F -HU_160 31 24.17 F -HU_162 50 29.03 F -HU_163 49 23.15 F -HU_164 45 25.63 F -HU_166 40 19.72 F -HU_167 55 20.57 F -HU_168 37 20.76 F -HU_169 53 19.14 F -HU_170 50 24.61 F -HU_171 29 21.37 F -HU_172 55 21.36 F -HU_173 55 20.28 F -HU_174 42 31.64 F -HU_175 35 21.26 F -HU_177 59 28.58 F -HU_179 33 26.57 F -HU_180 53 23.74 F -HU_181 49 22.46 F -HU_182 43 23.74 F -HU_183 46 19.13 F -HU_184 37 25.33 F -HU_185 42 21.09 F -HU_186 44 22.1 F -HU_187 21 19.95 F -HU_188 22 24.22 F -HU_189 39 19.43 F -HU_190 28 25.93 M -HU_191 36 26.12 M -HU_192 31 24.22 M -HU_193 35 21.78 F -HU_194 40 28.04 F -HU_195 26 18.42 F -HU_196 27 21.1 F -HU_197 26 20.72 M -HU_198 35 22.98 M -HU_199 33 21.04 M -HU_200 46 23.89 M -HU_201 34 20.24 M -HU_202 42 28.06 M -HU_203 25 19.95 F -HU_204 31 29.06 M -HU_205 33 28.37 M -HU_206 45 22.15 F -HU_207 33 19.47 F -HU_208 27 18.61 F -HU_209 17.5 21.48 F |
| b |
| diff -r 4ff502a46189 -r b2414be87d4b tests/sacurine/variableMetadata.tsv --- a/tests/sacurine/variableMetadata.tsv Sat Jul 30 12:21:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,110 +0,0 @@ - msiLevel hmdb chemicalClass -(2-methoxyethoxy)propanoic acid isomer 2 Organi -(gamma)Glu-Leu/Ile 2 AA-pep -1-Methyluric acid 1 HMDB03099 AroHeP:Xenobi -1-Methylxanthine 1 HMDB10738 AroHeP -1,3-Dimethyluric acid 1 HMDB01857 AroHeP -1,7-Dimethyluric acid 1 HMDB11103 AroHeP -2-acetamido-4-methylphenyl acetate 2 AroHoM -2-Aminoadipic acid 1 HMDB00510 AA-pep -2-Hydroxybenzyl alcohol 1 HMDB59709 AroHoM -2-Isopropylmalic acid 1 HMDB00402 Organi -2-Methylhippuric acid 1 HMDB11723 AA-pep:AcyGly -2,2-Dimethylglutaric acid 1 Lipids -3-Hydroxybenzyl alcohol 1 HMDB59712 AroHoM -3-Hydroxyphenylacetic acid 1 HMDB00440 AroHoM -3-Indole carboxylic acid glucuronide 2 HMDB13189 Carboh -3-Methyl-2-oxovaleric acid 1 HMDB00491 Lipids -3-Methylcrotonylglycine 1 HMDB00459 AA-pep:AcyGly -3,3-Dimethylglutaric acid 1 HMDB02441 Lipids -3,4-Dihydroxybenzeneacetic acid 1 HMDB01336 AroHoM -3,5-dihydroxybenzoic acid/3,4-dihydroxybenzoic acid 2 AroHoM -3,7-Dimethyluric acid 1 HMDB01982 AroHeP -4-Acetamidobutanoic acid isomer 2 2 Lipids -4-Acetamidobutanoic acid isomer 3 2 Lipids -4-Hydroxybenzoic acid 1 HMDB00500 AroHoM -4-Methylhippuric acid/3-Methylhippuric acid 1 AA-pep:AcyGly -5-Hydroxyindoleacetic acid 1 HMDB00763 AroHeP -5-Sulfosalicylic acid 1 HMDB11725 AroHoM -6-(2-hydroxyethoxy)-6-oxohexanoic acid 2 Organi -6-(carboxymethoxy)-hexanoic acid 2 Organi -9-Methylxanthine 2 HMDB59716 AroHeP -Acetaminophen glucuronide 1 HMDB10316 Carboh -Acetylphenylalanine 1 HMDB00512 AA-pep -alpha-N-Phenylacetyl-glutamine 1 HMDB06344 AA-pep -Aminosalicyluric acid 2 AA-pep:AcyGly -Asp-Leu/Ile isomer 1 2 AA-pep -Asp-Leu/Ile isomer 2 2 AA-pep -Aspartic acid 1 HMDB00191 AA-pep -Azelaic acid 1 HMDB00784 Organi -Benzoic acid isomer 2 AroHoM -Chenodeoxycholic acid isomer 2 Lipids:Steroi -Cinnamoylglycine 1 HMDB11621 AA-pep:AcyGly -Citric acid 1 HMDB00094 Organi -Dehydroepiandrosterone 3-glucuronide 1 HMDB10348 Lipids:Steroi -Dehydroepiandrosterone sulfate 1 HMDB01032 Lipids:Steroi -Deoxyhexose 1 HMDB00849 Carboh -Dimethylguanosine 2 HMDB04824 Nucleo -FMNH2 2 HMDB01142 AroHeP -Fumaric acid 1 HMDB00134 Lipids -Gentisic acid 1 HMDB00152 AroHoM -Glu-Val 2 HMDB59717 AA-pep -Gluconic acid and/or isomers 2 Carboh -Glucuronic acid and/or isomers 2 Carboh -Glyceric acid 1 HMDB00139 Carboh -Glycocholic acid isomer 2 2 Lipids:Steroi -Glycocholic acid isomer 3 2 Lipids:Steroi -Heptylmalonic acid 2 HMDB59719 Lipids -Hexanoylglycine 1 HMDB00701 AA-pep:AcyGly -Hippuric acid 1 HMDB00714 AA-pep:AcyGly -Hydroxybenzyl alcohol isomer 2 AroHeM -Hydroxyphenyllactic acid 1 HMDB00755 AroHoM -Hydroxysuberic acid isomer 1 2 Organi -Hydroxysuberic acid isomer 2 2 Organi -Isovalerylalanine isomer 2 AA-pep -Ketoleucine 1 HMDB00695 Lipids -Kynurenic acid 1 HMDB00715 AA-pep -Malic acid 1 HMDB00156 Organi -Methoxysalicylic acid isomer 2 AroHoM -Methyl (hydroxymethyl)pyrrolidine-carboxylate/Methyl (hydroxy)piperidine-carboxylate 2 AA-pep -Methylinosine 2 Nucleo -Mevalonic acid isomer 1 2 Organi -Monoethyl phthalate 2 HMDB02120 AroHoM:Xenobi -N-Acetyl-aspartic acid 1 HMDB00812 AA-pep -N-Acetylisoleucine 1 AA-pep -N-Acetylleucine 1 HMDB11756 AA-pep -N-Acetyltryptophan 1 HMDB13713 AA-pep -N-Acetyltryptophan isomer 3 2 AA-pep -N2-Acetylaminoadipic acid 2 AA-pep -N4-Acetylcytidine 1 HMDB05923 Nucleo -Nicotinuric acid isomer 2 AA-pep -Ortho-Hydroxyphenylacetic acid 1 HMDB00669 AroHoM -Oxoglutaric acid 2 HMDB00208 Organi -p-Anisic acid 1 HMDB01101 AroHoM -p-Hydroxyhippuric acid 2 HMDB13678 AA-pep:AcyGly -p-Hydroxymandelic acid 1 HMDB00822 AroHoM -p-Hydroxyphenylacetic acid 1 HMDB00020 AroHoM -Pantothenic acid 1 HMDB00210 AliAcy -Pentose 2 Carboh -Phe-Tyr-Asp (and isomers) 2 AA-pep -Porphobilinogen 1 HMDB00245 Organi -Pyridoxic acid isomer 1 2 AroHeM -Pyridylacetylglycine 2 HMDB59723 AA-pep:AcyGly:Xenobi -Pyrocatechol sulfate 2 HMDB59724 AroHoM -Pyroglutamic acid 1 HMDB00267 AliHeM -Pyrroledicarboxylic acid 2 AroHeM -Pyruvic acid 1 HMDB00243 Organi -Quinic acid 1 HMDB03072 AliHoM -Salicylic acid 1 HMDB01895 AroHoM:Xenobi -Sebacic acid 1 HMDB00792 Organi -Suberic acid 1 HMDB00893 Organi -Sulfosalicylic acid isomer 2 AroHoM -Taurine 1 HMDB00251 Organi -Testosterone glucuronide 2 HMDB03193 Lipids:Steroi -Tetrahydrohippuric acid 2 AA-pep:AcyGly -Threo-3-Phenylserine 1 HMDB02184 AA-pep -Threonic acid/Erythronic acid 2 Carboh -Tryptophan 1 HMDB00929 AA-pep -Valerylglycine isomer 1 2 AA-pep:AcyGly -Valerylglycine isomer 2 2 AA-pep:AcyGly -Xanthosine 1 HMDB00299 Nucleo |