read.bed.files {RnBeads} | R Documentation |
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 |
sample.sheet |
Optional file name containing a table of sample annotation data, or the table itself in the form
of a |
file.names.col |
Column of the sample sheet which contains the file names (integer singleton). If |
assembly |
Genome assembly. Defaults to human ( |
region.types |
|
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, |
skip.lines |
The number of top lines to skip while reading the BED files |
sep.samples |
|
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 |
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 |
To control the BED column assignment, one should also supply arguments to read.single.bed
.
an object of class RnBiseqSet
Pavlo Lutsik