exampleCAGEexp {CAGEr} | R Documentation |
Lazy-loaded example CAGEexp object, containing most of the CAGEr data structures created with the CAGEr modifier functions.
exampleCAGEexp
A CAGEexp object.
## Not run: pathsToInputFiles <- list.files( system.file("extdata", package = "CAGEr") , "ctss$" , full.names = TRUE) sampleLabels <- sub( ".chr17.ctss", "", basename(pathsToInputFiles)) exampleCAGEexp <- CAGEexp( genomeName = "BSgenome.Drerio.UCSC.danRer7" , inputFiles = pathsToInputFiles , inputFilesType = "ctss" , sampleLabels = sub( ".chr17.ctss", "", basename(pathsToInputFiles))) getCTSS(exampleCAGEexp) librarySizes(exampleCAGEexp) colData(exampleCAGEexp) exampleCAGEexp$l1 <- NULL exampleCAGEexp <- exampleCAGEexp[,c(5, 2, 1, 3, 4)] # Non-aplhabetic order may help catch bugs CTSStagCountSE(exampleCAGEexp) <- CTSStagCountSE(exampleCAGEexp)[1:5000,] # Slim the object exampleCAGEexp$librarySizes <- sapply(CTSStagCountDF(exampleCAGEexp), sum) # Repair metadata summariseChrExpr(exampleCAGEexp) annotateCTSS(exampleCAGEexp, exampleZv9_annot) CTSStoGenes(exampleCAGEexp) normalizeTagCount(exampleCAGEexp) clusterCTSS(exampleCAGEexp) cumulativeCTSSdistribution(exampleCAGEexp, "tagClusters") quantilePositions(exampleCAGEexp, "tagClusters") aggregateTagClusters(exampleCAGEexp) annotateConsensusClusters(exampleCAGEexp, exampleZv9_annot) cumulativeCTSSdistribution(exampleCAGEexp, "consensusClusters") quantilePositions(exampleCAGEexp, "consensusClusters") save(exampleCAGEexp, file = "data/exampleCAGEexp.RData", compress = "xz") ## End(Not run)