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

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

CAGEr class to hold all data and metadata about one CAGE experiment.

Description

The CAGEr class is a MultiAssayExperiment object containing all data and metadata about a set of CAGE libraries. It replaced the CAGEset class in 2017. 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

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.

exampleCAGEexp <- 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 <- CTSStagCountDF(exampleCAGEexp) |> sapply ( \(col) sum(col > 0) )
exampleCAGEexp$l1

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.