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]