Usage
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, ...)
Arguments
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