exampleCAGEexp {CAGEr}R Documentation

Example CAGEexp object.

Description

Lazy-loaded example CAGEexp object, containing most of the CAGEr data structures created with the CAGEr modifier functions.

Usage

exampleCAGEexp

Format

A CAGEexp object.

Examples

# 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)

[Package CAGEr version 1.24.0 Index]