read.bed.files: read.bed.files
In RnBeads: RnBeads

Description Usage Arguments Details Value Author(s)

Reads a reduced-representation/whole-genome bisulfite sequencing data set from a set of BED files

read.bed.files(
  base.dir = NULL,
  file.names = NULL,
  sample.sheet = NULL,
  file.names.col = 0,
  assembly = rnb.getOption("assembly"),
  region.types = rnb.region.types.for.analysis(assembly),
  pos.coord.shift = 1L,
  skip.lines = 1,
  sep.samples = rnb.getOption("import.table.separator"),
  merge.bed.files = TRUE,
  useff = rnb.getOption("disk.dump.big.matrices"),
  usebigff = rnb.getOption("disk.dump.bigff"),
  verbose = TRUE,
  ...
)

`base.dir`	Directory with BED files contatining processed methylation data
`file.names`	Optional non-empty `character` vector listing the names of the files that should be loaded relative to `base.dir`. If supplied, this vector must not contain `NA` among its elements.
`sample.sheet`	Optional file name containing a table of sample annotation data, or the table itself in the form of a `data.frame` or `matrix`. Only (and all) samples defined in this table will be loaded. The table is expected to contain a column named `"barcode"` that lists the samples' Sentrix barcodes. If such a column is not present, this function searches for columns `"Sentrix_ID"` and `"Sentrix_Position"` (or similar) that build a barcode.
`file.names.col`	Column of the sample sheet which contains the file names (integer singleton). If `NA` an attempt will be made to find a suiting column automatically.
`assembly`	Genome assembly. Defaults to human (`"hg19"`)
`region.types`	`character` vector storing the types of regions for which the methylation information is to be summarized. The function `rnb.region.types` provides the list of all supported regions. Setting this to `NULL` or an empty vector restricts the dataset to site methylation only.
`pos.coord.shift`	The frame shift between the the CpG annotation (1-based) and the coordinates in the loaded BEDs. If BEDs have 0-based coordinates, `pos.coord.shift=1` (default).
`skip.lines`	The number of top lines to skip while reading the BED files
`sep.samples`	`character` singleton used as field separator in the sample sheet file. Default value is taken by the call to `rnb.getOption("import.table.separator")`
`merge.bed.files`	In case multiple BED files are specified for each sample, the flag indicates whether the methylation calls should be merged after reading
`useff`	If `TRUE`, functionality provided by the `ff` package will be used to read the data efficiently.
`usebigff`	flag specifying whether the extended ff functionality should be used (large matrix support for ff)
`verbose`	Flag indicating ifthe messages to the logger should be sent. Note that the logger must be initialized prior to calling this function. Logging is useful for keeping a record of the downloaded and processed samples. Also, informative messages are stored in case of an error.
`...`	Further arguments which are passed to the internal function `read.single.bed` and to `read.table`