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$" , full.names = TRUE) sampleLabels <- sub( ".chr17.ctss", "", basename(pathsToInputFiles)) exampleCAGEexp <- CAGEexp( genomeName = "BSgenome.Drerio.UCSC.danRer7" , inputFiles = pathsToInputFiles , inputFilesType = "ctss" , sampleLabels = sub( ".chr17.ctss", "", basename(pathsToInputFiles))) exampleCAGEexp <- getCTSS(exampleCAGEexp) librarySizes(exampleCAGEexp) colData(exampleCAGEexp) exampleCAGEexp$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 exampleCAGEexp <- summariseChrExpr(exampleCAGEexp) |> annotateCTSS(exampleZv9_annot) |> CTSStoGenes() |> normalizeTagCount() |> getExpressionProfiles("CTSS") |> clusterCTSS() |> cumulativeCTSSdistribution("tagClusters") |> quantilePositions("tagClusters") |> aggregateTagClusters() |> annotateConsensusClusters(exampleZv9_annot) |> cumulativeCTSSdistribution("consensusClusters") |> quantilePositions("consensusClusters") |> getExpressionProfiles("consensusClusters") save(exampleCAGEexp, file = "data/exampleCAGEexp.RData", compress = "xz") ## End(Not run)