Mercurial > repos > yufei-luo > s_mart

diff SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,38 @@
+# RNAseqFunctions
+# when sourced, sources all R functions associated with RNAseq data analysis
+
+RNAseqFunctions <- function( RfuncDir ){
+  
+  source(paste(RfuncDir, "loadTargetFile.R", sep=""))
+  source(paste(RfuncDir, "loadCountData.R", sep=""))
+# source(paste(RfuncDir, "loadStrandData.R", sep=""))
+  source(paste(RfuncDir, "HTseqClean.R", sep=""))
+  source(paste(RfuncDir, "raw2counts.R", sep=""))
+  source(paste(RfuncDir, "barplotTC.R", sep=""))
+  source(paste(RfuncDir, "barplotNul.R", sep=""))
+  source(paste(RfuncDir, "removeNul.R", sep=""))
+  source(paste(RfuncDir, "densityPlot.R", sep=""))
+  source(paste(RfuncDir, "boxplotCounts.R", sep=""))
+  source(paste(RfuncDir, "majSequence.R", sep=""))
+  source(paste(RfuncDir, "clusterPlot.R", sep=""))
+  source(paste(RfuncDir, "pairwiseSERE.R", sep=""))
+  source(paste(RfuncDir, "pairwiseScatterPlots.R", sep=""))
+#  source(paste(RfuncDir, "pairwiseScatterPlotsAll.R", sep=""))
+  source(paste(RfuncDir, "plotDispEstimates.R", sep=""))
+#  source(paste(RfuncDir, "deseqByCond.R", sep="")) 
+#  source(paste(RfuncDir, "edgeRByCond.R", sep=""))  
+#  source(paste(RfuncDir, "fisher.R", sep=""))
+  source(paste(RfuncDir, "histoRawp.R", sep=""))
+#  source(paste(RfuncDir, "histoRawpMconds.R", sep=""))
+  source(paste(RfuncDir, "MAplotDE.R", sep=""))
+#  source(paste(RfuncDir, "MAplotDEMconds.R", sep=""))
+  source(paste(RfuncDir, "exportComplete.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteEdgeR.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteFisher.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteMconds.R", sep=""))
+#  source(paste(RfuncDir, "exportCompleteByCond.R", sep=""))
+#  source(paste(RfuncDir, "exportCompletePaired.R", sep=""))
+  source(paste(RfuncDir, "exportDiff.R", sep=""))
+#  source(paste(RfuncDir, "synthese.R", sep=""))
+#  source(paste(RfuncDir, "exportDiffByCond.R", sep=""))
+}