Mercurial > repos > yufei-luo > s_mart

annotate SMART/DiffExpAnal/DESeqTools/RNAseqFunctions.R @ 32:3441fe98a2ba

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author m-zytnicki
date Tue, 30 Apr 2013 14:34:10 -0400
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1 # RNAseqFunctions
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2 # when sourced, sources all R functions associated with RNAseq data analysis
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3
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4 RNAseqFunctions <- function( RfuncDir ){
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5
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6 source(paste(RfuncDir, "loadTargetFile.R", sep=""))
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7 source(paste(RfuncDir, "loadCountData.R", sep=""))
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8 # source(paste(RfuncDir, "loadStrandData.R", sep=""))
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9 source(paste(RfuncDir, "HTseqClean.R", sep=""))
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10 source(paste(RfuncDir, "raw2counts.R", sep=""))
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11 source(paste(RfuncDir, "barplotTC.R", sep=""))
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12 source(paste(RfuncDir, "barplotNul.R", sep=""))
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13 source(paste(RfuncDir, "removeNul.R", sep=""))
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14 source(paste(RfuncDir, "densityPlot.R", sep=""))
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15 source(paste(RfuncDir, "boxplotCounts.R", sep=""))
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16 source(paste(RfuncDir, "majSequence.R", sep=""))
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17 source(paste(RfuncDir, "clusterPlot.R", sep=""))
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18 source(paste(RfuncDir, "pairwiseSERE.R", sep=""))
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19 source(paste(RfuncDir, "pairwiseScatterPlots.R", sep=""))
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20 # source(paste(RfuncDir, "pairwiseScatterPlotsAll.R", sep=""))
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21 source(paste(RfuncDir, "plotDispEstimates.R", sep=""))
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22 # source(paste(RfuncDir, "deseqByCond.R", sep=""))
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23 # source(paste(RfuncDir, "edgeRByCond.R", sep=""))
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24 # source(paste(RfuncDir, "fisher.R", sep=""))
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25 source(paste(RfuncDir, "histoRawp.R", sep=""))
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26 # source(paste(RfuncDir, "histoRawpMconds.R", sep=""))
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27 source(paste(RfuncDir, "MAplotDE.R", sep=""))
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28 # source(paste(RfuncDir, "MAplotDEMconds.R", sep=""))
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29 source(paste(RfuncDir, "exportComplete.R", sep=""))
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30 # source(paste(RfuncDir, "exportCompleteEdgeR.R", sep=""))
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31 # source(paste(RfuncDir, "exportCompleteFisher.R", sep=""))
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32 # source(paste(RfuncDir, "exportCompleteMconds.R", sep=""))
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33 # source(paste(RfuncDir, "exportCompleteByCond.R", sep=""))
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34 # source(paste(RfuncDir, "exportCompletePaired.R", sep=""))
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35 source(paste(RfuncDir, "exportDiff.R", sep=""))
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36 # source(paste(RfuncDir, "synthese.R", sep=""))
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37 # source(paste(RfuncDir, "exportDiffByCond.R", sep=""))
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38 }