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

    ## 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)

[Package CAGEr version 1.30.3 Index]