Mercurial > repos > artbio > fishertest
changeset 0:5f784a95ce13 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit 7d954797362ea5de843d812cb823ac1dd869e1df
| author | artbio |
|---|---|
| date | Mon, 28 Aug 2017 13:25:56 -0400 |
| parents | |
| children | 3a67bee2ef63 |
| files | fisher_test.xml test-data/counts.tab test-data/fisher.tab |
| diffstat | 3 files changed, 1074 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fisher_test.xml Mon Aug 28 13:25:56 2017 -0400 @@ -0,0 +1,74 @@ +<tool id="fishertest" name="Fisher's exact test" version="1.0.0"> + <description>on two gene hit lists</description> + <requirements> +<!-- <requirement type="package" version="3.1.2">R</requirement> --> + <requirement type="package" version="2.4.2=r3.3.1_0">bioconductor-qvalue</requirement> + </requirements> + <command><![CDATA[ + Rscript '$fisher_test' "\${GALAXY_SLOTS:-1}" + ]]></command> + <configfiles> + <configfile name="fisher_test"> + <![CDATA[ + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + options(warn=-1) + suppressMessages(library(qvalue)) + library(parallel) + args = commandArgs(trailingOnly = TRUE) + slots = as.numeric(args[1]) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE, stringsAsFactor = TRUE) + depth1 = sum(countsTable[,2]) + depth2 = sum(countsTable[,3]) + float_table=data.frame(countsTable[,2], countsTable[,3]) + + calc_pvalue <- function(row, depth1, depth2, ... ){ + thearray = array( c(row, (depth1 - row[1]), (depth2 - row[2])), dim=c(2,2)) + current_test = fisher.test( thearray ) + return(current_test\$p.value) + } + + cl <- makePSOCKcluster(slots) + clusterExport(cl=cl, varlist=c("calc_pvalue", "depth1", "depth2")) + ptm <- proc.time() + p_val = parApply(cl, float_table, 1, function(x) calc_pvalue(x, depth1, depth2)) + stopCluster(cl) + proc.time() - ptm + p_val[p_val>1]=1 + p = qvalue(p_val) + finalTable = cbind(countsTable, data.frame(p\$pvalues), data.frame(p\$qvalues)) + write.table ( finalTable, file = "${output}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + ]]> + </configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="gene hit lists, 2 samples"/> + </inputs> + <outputs> + <data name="output" format="tabular" label="Fisher test p-values" /> + </outputs> +<tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <output name="output" file="fisher.tab" ftype="tabular"/> + </test> +</tests> +<help> + +**What it does** + +Runs Fisher's exact test for testing the null of independence of rows and columns in a contingency table of two columns. + +p.pvalues: the chance of getting this data if it is independent between columns (false negative); the p-value. + +q.qvalues: FDR (Faslse Detection Rate) adjusted p-values; a q-value of 0.05 implies that 5% of significant tests will result in false positives. + +Be aware that this test does not take into account the biological noise that would be visible if replicates were available. + + +</help> +<citations> + <citation type="doi">10.1111/1467-9868.00346</citation> +</citations> + +</tool>
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