annotate deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/RNAseqFunctions.R @ 10:6e573fd3c41b draft

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# Marie-Anges Dillies
# 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=""))
}