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.
# The example commands in the CAGEexp help page were used to create the example # CAGEexp object used below. ## Not run: 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)