Mercurial > repos > yufei-luo > s_mart

comparison 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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17:b0e8584489e6 18:94ab73e8a190
1 # RNAseqFunctions
2 # when sourced, sources all R functions associated with RNAseq data analysis
3
4 RNAseqFunctions <- function( RfuncDir ){
5
6 source(paste(RfuncDir, "loadTargetFile.R", sep=""))
7 source(paste(RfuncDir, "loadCountData.R", sep=""))
8 # source(paste(RfuncDir, "loadStrandData.R", sep=""))
9 source(paste(RfuncDir, "HTseqClean.R", sep=""))
10 source(paste(RfuncDir, "raw2counts.R", sep=""))
11 source(paste(RfuncDir, "barplotTC.R", sep=""))
12 source(paste(RfuncDir, "barplotNul.R", sep=""))
13 source(paste(RfuncDir, "removeNul.R", sep=""))
14 source(paste(RfuncDir, "densityPlot.R", sep=""))
15 source(paste(RfuncDir, "boxplotCounts.R", sep=""))
16 source(paste(RfuncDir, "majSequence.R", sep=""))
17 source(paste(RfuncDir, "clusterPlot.R", sep=""))
18 source(paste(RfuncDir, "pairwiseSERE.R", sep=""))
19 source(paste(RfuncDir, "pairwiseScatterPlots.R", sep=""))
20 # source(paste(RfuncDir, "pairwiseScatterPlotsAll.R", sep=""))
21 source(paste(RfuncDir, "plotDispEstimates.R", sep=""))
22 # source(paste(RfuncDir, "deseqByCond.R", sep=""))
23 # source(paste(RfuncDir, "edgeRByCond.R", sep=""))
24 # source(paste(RfuncDir, "fisher.R", sep=""))
25 source(paste(RfuncDir, "histoRawp.R", sep=""))
26 # source(paste(RfuncDir, "histoRawpMconds.R", sep=""))
27 source(paste(RfuncDir, "MAplotDE.R", sep=""))
28 # source(paste(RfuncDir, "MAplotDEMconds.R", sep=""))
29 source(paste(RfuncDir, "exportComplete.R", sep=""))
30 # source(paste(RfuncDir, "exportCompleteEdgeR.R", sep=""))
31 # source(paste(RfuncDir, "exportCompleteFisher.R", sep=""))
32 # source(paste(RfuncDir, "exportCompleteMconds.R", sep=""))
33 # source(paste(RfuncDir, "exportCompleteByCond.R", sep=""))
34 # source(paste(RfuncDir, "exportCompletePaired.R", sep=""))
35 source(paste(RfuncDir, "exportDiff.R", sep=""))
36 # source(paste(RfuncDir, "synthese.R", sep=""))
37 # source(paste(RfuncDir, "exportDiffByCond.R", sep=""))
38 }