Nothing
## ----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")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.