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
DataFrame objects of
Rle-encoded expression values, instead of plain
data.frames. With large datasets, this saves considerable amounts of memory.
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
Sample labels must be syntactically valid in the sense of the
function, because they will be used as column names in some tables.
A list that must at least contain a
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.