Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

view DiffExpAnal/DESeqTools/RNAseqFunctions.R @ 0:63799b789162 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yufei-luo
date Tue, 22 Jan 2013 10:07:03 -0500
parents
children
line wrap: on
line source

# 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=""))
}