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Read collapsed single-molecule footprinting data from a bedMethyl file.

Source: R/readBedMethyl.R
readBedMethyl.Rd

This function will read collapsed single-molecule footprinting data (reads combined per genomic position) from a bedMethyl file.

Usage

readBedMethyl(
  fnames,
  modbase = NULL,
  nrows = Inf,
  seqinfo = NULL,
  sequence.context.width = 0,
  sequence.reference = NULL,
  ncpu = 1L,
  verbose = FALSE
)

Arguments

fnames

Character vector with one or several paths of bedMethyl files, such as generated by modkit pileup. Each file will be read separately and become one of the columns in the returned SummarizedExperiment object. If fnames is a named vector, the names are used as column names in the returned object. Otherwise, the column names will be s1, ..., sN, where N is the length of fnames. If several elements of fnames have identical names, the data from the corresponding files are summed into a single column in the returned object.

modbase

Character vector defining the modified base (or bases) to read. Useful for reading a subset of the data from bedMethyl files that contain multiple types of modified bases. If NULL (the default), all rows in the input file are read.

nrows

Only read nrows rows of the input file.

seqinfo

NULL or a Seqinfo object containing information about the set of genomic sequences (chromosomes). Alternatively, a named numeric vector with genomic sequence names and lengths. Useful to set the sorting order of sequence names.

sequence.context.width, sequence.reference

Define the sequence context to be extracted around modified bases. By default ( sequence.context.width = 0), no sequence context will be extracted, otherwise it will be returned in rowData(x)$sequence.context. See addSeqContext for details.

ncpu

A numeric scalar giving the number of parallel CPU threads to to use for some of the steps in readBedMethyl().

verbose

If TRUE, report on progress.

Value

A SummarizedExperiment object with genomic positions in rows and samples (the unique names of fnames) in the columns. If sequence.context.width != 0, rowData(x)$sequence.context will be a DNAStringSet object with the extracted sequences.

See also

modkit software, bedMethyl format description, SummarizedExperiment for the returned object type, fread for the function used to read the input files, addSeqContext used to add the sequence context.

Author

Michael Stadler

Examples

bmfile <- system.file("extdata", "modkit_pileup_1.bed.gz", package = "footprintR")
readBedMethyl(bmfile)
#> class: RangedSummarizedExperiment 
#> dim: 10000 1 
#> metadata(0):
#> assays(2): Nmod Nvalid
#> rownames: NULL
#> rowData names(0):
#> colnames(1): s1
#> colData names(0):