# HG changeset patch # User drosofff # Date 1489080663 18000 # Node ID 8cb991523c5a46086ce8b6f08a94c01c140ead88 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fisher_test commit f9c229fc39114e80cf01383d7240e4971b2e3c53 diff -r 000000000000 -r 8cb991523c5a fisher_test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fisher_test.xml Thu Mar 09 12:31:03 2017 -0500 @@ -0,0 +1,75 @@ + + on two gene hit lists + + R + biocbasics + bioconductor-qvalue + + + + + 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") + ]]> + + + + + + + + + + + + + + + + +**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. + + + + + 10.1111/1467-9868.00346 + + + diff -r 000000000000 -r 8cb991523c5a test-data/counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Thu Mar 09 12:31:03 2017 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 4: Pronuclei 1: accepted_hits +NM_001195025 0 0 +NM_028778 0 0 +NM_001290393 0 0 +NM_008922 3133 2288 +NM_175370 4 7 +NM_001290390 0 0 +NM_175642 977 1013 +NM_001290392 0 0 +NM_027671 0 0 +NM_178884 0 0 +NM_199021 332 1436 +NM_198680 0 0 +NM_011465 0 0 +NM_130890 0 0 +NM_001113393 0 0 +NM_001113392 0 0 +NM_001113391 19 88 +NM_031162 0 0 +NR_103716 0 0 +NM_001160371 0 0 +NM_177834 1 2 +NM_145381 606 367 +NM_177173 0 0 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