exampleCAGEexp: Example CAGEexp object.

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.