CAGEexp-class: CAGEr class to hold all data and metadata about one CAGE...

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

Description

The CAGEr class is a MultiAssayExperiment object containing all data and metadata about a set of CAGE libraries. It is a replacement for the CAGEset class. The main difference is that the expression data is stored in DataFrame objects of Rle-encoded expression values, instead of plain data.frames. With large datasets, this saves considerable amounts of memory.

Details

If genomeName is NULL, checks of chromosome names will be disabled and G-correction will not be possible. See https://support.bioconductor.org/p/86437/ for an example on how to create a BSgenome package.

Sample labels must be syntactically valid in the sense of the make.names() function, because they will be used as column names in some tables.

Slots

metadata

A list that must at least contain a genomeName member.

See Also

CAGEset, make.names

Examples

pathsToInputFiles <- list.files( system.file("extdata", package = "CAGEr")
                               , "ctss$"
                               , full.names = TRUE)
sampleLabels <- sub( ".chr17.ctss", "", basename(pathsToInputFiles))

# The CAGEexp object can be created using specific constructor commands
                              
exampleCAGEexp <-
  CAGEexp( genomeName     = "BSgenome.Drerio.UCSC.danRer7"
         , inputFiles     = pathsToInputFiles
         , inputFilesType = "ctss"
         , sampleLabels   = sub( ".chr17.ctss", "", basename(pathsToInputFiles)))
         
# Alternatively, it can be created just like another MultiAssayExperiment.
# This is useful when providing pre-existing colData with many columns.

exampleCAGEexp <-
  CAGEexp( metadata = list(genomeName = "BSgenome.Drerio.UCSC.danRer7")
         , colData  = DataFrame( inputFiles     = pathsToInputFiles
                               , sampleLabels   = sampleLabels
                               , inputFilesType = "ctss"
                               , row.names      = sampleLabels))


# Expression data is loaded by the getCTSS() function, that also calculates
# library sizes and store them in the object's column data.

getCTSS(exampleCAGEexp)
librarySizes(exampleCAGEexp)
colData(exampleCAGEexp)

# CTSS data is stored internally as a SummarizedExperiemnt that can be retreived
# as a whole, or as GRanges, or as an expression DataFrame.

CTSStagCountSE(exampleCAGEexp)
CTSScoordinatesGR(exampleCAGEexp)
CTSStagCountDF(exampleCAGEexp)

# Columns of the "colData" table are accessible directly via the "$" operator.

exampleCAGEexp$l1 <- colSums(CTSStagCountDf(exampleCAGEexp) > 0)
exampleCAGEexp$l1

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