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$"
                                   , full.names = TRUE)
    sampleLabels <- sub( ".chr17.ctss", "", basename(pathsToInputFiles))
    exampleCAGEexp <-
      CAGEexp( genomeName     = "BSgenome.Drerio.UCSC.danRer7"
             , inputFiles     = pathsToInputFiles
             , inputFilesType = "ctss"
             , sampleLabels   = sub( ".chr17.ctss", "", basename(pathsToInputFiles)))
    exampleCAGEexp <- getCTSS(exampleCAGEexp)
    librarySizes(exampleCAGEexp)
    colData(exampleCAGEexp)
    exampleCAGEexp$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)

[Package CAGEr version 2.0.2 Index]