GDS_Vignette.R
In GDS: Genome-Wide Differential Splicing Detection

### R code from vignette source 'GDS_Vignette.Rnw'

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### code chunk number 1: DataProcessing (eval = FALSE)
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## DataProcessing(chipType="HuEx-1_0-st-v2",tags="coreR3,A20071112,EP",
##                Name="TissueData",ExonSummarization=TRUE,GeneSummarization=TRUE,
##                FIRMA=TRUE,location="TissueData",verbose=TRUE)


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### code chunk number 2: PivotTransformation (eval = FALSE)
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## load("TissueData/TissueData.RData")
## 
## PivotTransformation(Data=TissueData,GeneID=TissueData$GeneID,
##                     ExonID=TissueData$ExonID,savecsv=TRUE,
##                     Name="TissueData_Pivot",location="TissueData")


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### code chunk number 3: GDS (eval = FALSE)
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## load("TissueData/TissueData.RData")
## 
## GDS_Output=GDSFunction(geneData=TissueData,nsim=5000,geneID=TissueData$GeneID,
##                        exonID=TissueData$ExonID,informativeCalls=TRUE,alpha=0.5)


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### code chunk number 4: Search (eval = FALSE)
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## exonID <- c(3252129,3597384,3333718,3735208,2598321,3338589,2605391,2605390,
##             2605386,3025632,2375766,3569827,3569830,2334499,3972987,2516011,
##             2989068,3422189)
## 
## load("GDS_Output.RData")
## 
## Results=Search(WhatToLookFor=data.frame(ExonID=exonID),Data=GDS_Output, 
##                AggregateResults=FALSE,NotFound=NULL)


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### code chunk number 5: ExonTesting (eval = FALSE)
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## load("TissueData/GDS_Output.RData")
## 
## groupHMPT=c(7,8,9,16,17,18,22,23,24,31,32,33)
## groupOthers=c(1,2,3,4,5,6,10,11,12,13,14,15,19,20,21,25,26,27,28,29,30)
## groups=list(group1=groupHMPT,group2=groupOthers)
## 
## TissueData_ExonTesting=ExonTesting(Data=GDS_Output,Exonthreshold=NULL,groups=groups,
##                                    paired=FALSE,significancelevel=NULL)


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### code chunk number 6: ASExons (eval = FALSE)
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## TissueData_ExonTesting_Sign1=ASExons(Data=GDS_Output,Exonthreshold=0.5,groups=groups,
##                                      paired=FALSE,significancelevel=0.05)
## 
## TissueData_ExonTesting_Sign2=ASExons(Data=TissueData_ExonTesting,Exonthreshold=0.5,
##                                      groups=groups,paired=FALSE,significancelevel=0.05)


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### code chunk number 7: FIRMAScores (eval = FALSE)
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## load("TissueData/FIRMA_Output.RData")
## load("TissueData/GDS_Output.RData")
## 
## groupHMPT=c(7,8,9,16,17,18,22,23,24,31,32,33)
## groupOthers=c(1,2,3,4,5,6,10,11,12,13,14,15,19,20,21,25,26,27,28,29,30)
## groups=list(group1=groupHMPT,group2=groupOthers)
## 
## exons=TissueData_ExonTesting[which(TissueData_ExonTesting$X50.>0.5),]
## 
## TissueData_FIRMA=FIRMAScores(Data=FIRMA_Output,InformativeExons=exons,
##                              groups=groups,paired=FALSE,significancelevel=0.05)


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### code chunk number 8: PlotFunction (eval = FALSE)
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## #Top gene 2736322 and   Top exon 2736397
## load("TissueData/TissueData.rda")
## load("TissueData/TissueData_ExonLevelSummarized.RData")
## load("TissueData/TissueData_GeneLevelSummarized.RData")
## load("TissueData/FIRMA_Output.RData")
## load("TissueData/GDS_Output.RData") 
## 
## groupHMPT=c(7,8,9,16,17,18,22,23,24,31,32,33)
## groupOthers=c(1,2,3,4,5,6,10,11,12,13,14,15,19,20,21,25,26,27,28,29,30)
## groups=list(group1=groupHMPT,group2=groupOthers)
## 
## PlotFunction(GeneID="2736322",ExonID="2736397",Data=TissueData,
##              GDS_Output=GDS_Output,GeneLevelData=TissueData_GeneLevelSummarized,
##              ExonLevelData=TissueData_ExonLevelSummarized,FIRMA_Data=FIRMA_Output,
##              groups=groups,plottype="new",
##              location="TissueData/Gene2736322_Exon2736397")
## 


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### code chunk number 9: SpliceIndex (eval = FALSE)
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## load("TissueData/TissueData_ExonLevelSummarized.RData")
## load("TissueData/TissueData_GeneLevelSummarized.RData")
## 
## 
## groupHMPT=c(7,8,9,16,17,18,22,23,24,31,32,33)
## groupOthers=c(1,2,3,4,5,6,10,11,12,13,14,15,19,20,21,25,26,27,28,29,30)
## groups=list(group1=groupHMPT,group2=groupOthers)
## 
## 
## SI_Output=SpliceIndex(GeneData=TissueData_ExonLevelSummarized,
##                       ExonData=TissueData_GeneLevelSummarized,
##                       InformativeExons=NULL,groups=groups,
##                       paired=FALSE,significancelevel=NULL)


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### code chunk number 10: sessionInfo
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toLatex(sessionInfo())