BEDFile objects
These functions support the import and export of the UCSC BED format and its variants, including BEDGraph.
## S4 method for signature 'BEDFile,ANY,ANY'
import(con, format, text, trackLine = TRUE,
genome = NA, colnames = NULL,
which = NULL, seqinfo = NULL, extraCols = character(),
sep = c("\t", ""), na.strings=character(0L))
import.bed(con, ...)
import.bed15(con, ...)
import.bedGraph(con, ...)
## S4 method for signature 'ANY,BEDFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'GenomicRanges,BEDFile,ANY'
export(object, con, format,
append = FALSE, index = FALSE,
ignore.strand = FALSE, trackLine = NULL)
## S4 method for signature 'UCSCData,BEDFile,ANY'
export(object, con, format,
trackLine = TRUE, ...)
export.bed(object, con, ...)
export.bed15(object, con, ...)
## S4 method for signature 'GenomicRanges,BED15File,ANY'
export(object, con, format,
expNames = NULL, trackLine = NULL, ...)
export.bedGraph(object, con, ...)con |
A path, URL, connection or |
object |
The object to export, should be a |
format |
If not missing, should be one of “bed”, “bed15”, “bedGraph”, “bedpe”, “narrowPeak” or “broadPeak”. |
text |
If |
trackLine |
For import, an imported track line will be stored
in a |
genome |
The identifier of a genome, or a |
colnames |
A character vector naming the columns to parse. These should name columns in the result, not those in the BED spec, so e.g. specify “thick”, instead of “thickStart”. |
which |
A |
index |
If |
ignore.strand |
Whether to output the strand when not required (by the existence of later fields). |
seqinfo |
If not |
extraCols |
A character vector in the same form as
|
sep |
A character vector with a single character indicating the
field separator, like |
na.strings |
Character vector with strings, appended to the
standard |
append |
If |
expNames |
character vector naming columns in
|
... |
Arguments to pass down to methods to other methods. For
import, the flow eventually reaches the |
The BED format is a tab-separated table of intervals, with annotations like name, score and even sub-intervals for representing alignments and gene models. Official (UCSC) child formats currently include BED15 (adding a number matrix for e.g. expression data across multiple samples) and BEDGraph (a compressed means of storing a single score variable, e.g. coverage; overlapping features are not allowed). Many tools and organizations have extended the BED format with additional columns for particular use cases. The advantage of BED is its balance between simplicity and expressiveness. It is also relatively scalable, because only the first three columns (chrom, start and end) are required. Thus, BED is best suited for representing simple features. For specialized cases, one is usually better off with another format. For example, genome-scale vectors belong in BigWig, alignments from high-throughput sequencing belong in BAM, and gene models are more richly expressed in GFF.
The following is the mapping of BED elements to a GRanges object.
NA values are allowed only where indicated.
These appear as a “.” in the file. Only the first three columns
(chrom, start and strand) are required. The other columns can only be
included if all previous columns (to the left) are included. Upon export,
default values are used to automatically pad the table, if necessary.
the ranges component.
character vector (NA's allowed) in the name
column; defaults to NA on export.
numeric vector in the score
column, accessible via the score accessor. Defaults to 0
on export. This is the only column present in BEDGraph (besides
chrom, start and end), and it is required.
strand factor (NA's allowed) in the strand
column, accessible via the strand accessor; defaults to NA
on export.
IntegerRanges object in a
column named thick; defaults to the ranges of the feature
on export.
an integer matrix of color codes, as returned by
col2rgb, or any valid input to
col2rgb, in the itemRgb column; default is NA
on export, which translates to black.
IntegerRangesList
object in a column named blocks; defaults to empty upon BED15
export.
For BED15 files, there should be a column of scores in
mcols(object) for each sample in the experiment. The columns
are named according to the expNames (found in the file, or
passed as an argument during export). NA scores are stored as
“-10000” in the file.
For a “bedpe” file, a Pairs object combining two
GRanges. The name and score are carried over to
the metadata columns.
Otherwise, a GRanges with the metadata columns described in the
details.
To import one of the multitude of BEDX+Y formats, such as those used
to distribute ENCODE data through UCSC (narrowPeaks, etc), specify
the extraCols argument to indicate the expected names and
classes of the special columns. We assume that the
last length(extraCols) columns are special, and that the
preceding columns adhere to the BED format. “narrowPeak”
and “broadPeak” types are handled explicitly by specifying
these types as the format argument, rather than by
using extraCols.
The BEDFile class extends RTLFile and is a
formal represention of a resource in the BED format.
To cast a path, URL or connection to a BEDFile, pass it to
the BEDFile constructor. Classes and constructors also exist
for the subclasses BED15File, BEDGraphFile and
BEDPEFile.
Michael Lawrence
test_path <- system.file("tests", package = "rtracklayer")
test_bed <- file.path(test_path, "test.bed")
test <- import(test_bed)
test
test_bed_file <- BEDFile(test_bed)
import(test_bed_file)
test_bed_con <- file(test_bed)
import(test_bed_con, format = "bed")
import(test_bed, trackLine = FALSE)
import(test_bed, genome = "hg19")
import(test_bed, colnames = c("name", "strand", "thick"))
which <- GRanges("chr7:1-127473000")
import(test_bed, which = which)
bed15_file <- file.path(test_path, "test.bed15")
bed15 <- import(bed15_file)
## Not run:
test_bed_out <- file.path(tempdir(), "test.bed")
export(test, test_bed_out)
test_bed_out_file <- BEDFile(test_bed_out)
export(test, test_bed_out_file)
export(test, test_bed_out, name = "Alternative name")
test_bed_gz <- paste(test_bed_out, ".gz", sep = "")
export(test, test_bed_gz)
export(test, test_bed_out, index = TRUE)
export(test, test_bed_out, index = TRUE, trackLine = FALSE)
bed_text <- export(test, format = "bed")
test <- import(format = "bed", text = bed_text)
test_bed15_out <- file.path(tempdir(), "test.bed15")
export(bed15, test_bed15_out) # UCSCData knows the expNames
export(as(bed15, "GRanges"), test_bed15_out, # have to specify expNames
expNames=paste0("breast_", c("A", "B", "C")))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.