## ----eval=TRUE----------------------------------------------------------- library("TSRchitect") ## ----eval=FALSE---------------------------------------------------------- # TSRchitectUsersGuide() ## ----eval=TRUE----------------------------------------------------------- extdata.dir <- system.file("extdata/bamFiles", package="TSRchitect") tssObjectExample <- loadTSSobj(experimentTitle="Vignette Example", inputDir=extdata.dir, n.cores=1, isPairedBAM=TRUE, sampleNames=c("sample1-rep1", "sample1-rep2","sample2-rep1", "sample2-rep2"), replicateIDs=c(1,1,2,2)) #datasets 1-2 and 3-4 are replicates ## ----eval=FALSE---------------------------------------------------------- # tssObjectExample ## ----eval=TRUE----------------------------------------------------------- tssObjectExample <- inputToTSS(experimentName=tssObjectExample) tssObjectExample <- processTSS(experimentName=tssObjectExample, n.cores=1, tssSet="all", writeTable=FALSE) ## ----eval=TRUE----------------------------------------------------------- tssObjectExample <- determineTSR(experimentName=tssObjectExample, n.cores=1, tssSetType="replicates", tssSet="all", tagCountThreshold=25, clustDist=20, writeTable=FALSE) ## ----eval=TRUE----------------------------------------------------------- tssObjectExample <- mergeSampleData(experimentName=tssObjectExample, n.cores=1, tagCountThreshold=1) tssObjectExample <- determineTSR(experimentName=tssObjectExample, n.cores=1, tssSetType="merged", tssSet="all", tagCountThreshold=25, clustDist=20, writeTable=FALSE) tssObjectExample <- addTagCountsToTSR(experimentName=tssObjectExample, tsrSetType="merged", tsrSet=1, tagCountThreshold=25, writeTable=FALSE) ## ----eval=TRUE----------------------------------------------------------- sample_1_1_tsrs <- getTSRdata(experimentName=tssObjectExample, slotType="replicates", slot=1) print(sample_1_1_tsrs) ## ----eval=TRUE----------------------------------------------------------- gff3data.dir <- system.file("extdata", package="TSRchitect") tssObjectExample <- importAnnotationExternal(experimentName=tssObjectExample, fileType="gff3", annotFile=paste(gff3data.dir,"gencode.v19.chr22.transcript.gff3",sep="/")) tssObjectExample <- addAnnotationToTSR(experimentName=tssObjectExample, tsrSetType="merged", tsrSet=1, upstreamDist=2000, downstreamDist=500, feature="transcript", featureColumnID="ID", writeTable=FALSE) ## ----eval=FALSE---------------------------------------------------------- # save(tssObjectExample, file="tssObjectExample.RData")