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BEDFile-class

BEDFile objects


Description

These functions support the import and export of the UCSC BED format and its variants, including BEDGraph.

Usage

## 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, ...)

Arguments

con

A path, URL, connection or BEDFile object. For the functions ending in .bed, .bedGraph and .bed15, the file format is indicated by the function name. For the base export and import functions, the format must be indicated another way. If con is a path, URL or connection, either the file extension or the format argument needs to be one of “bed”, “bed15”, “bedGraph”, “bedpe”, “narrowPeak”, or “broadPeak”. Compressed files (“gz”, “bz2” and “xz”) are handled transparently.

object

The object to export, should be a GRanges or something coercible to a GRanges. If targeting the BEDPE format, this should be something coercible to Pairs. If the object has a method for asBED (like GRangesList), it is called prior to coercion. This makes it possible to export a GRangesList or TxDb in a way that preserves the hierarchical structure. For exporting multiple tracks, in the UCSC track line metaformat, pass a GenomicRangesList, or something coercible to one.

format

If not missing, should be one of “bed”, “bed15”, “bedGraph”, “bedpe”, “narrowPeak” or “broadPeak”.

text

If con is missing, a character vector to use as the input

trackLine

For import, an imported track line will be stored in a TrackLine object, as part of the returned UCSCData. For the UCSCData method on export, whether to output the UCSC track line stored on the object, for the other export methods, the actual TrackLine object to export.

genome

The identifier of a genome, or a Seqinfo, or NA if unknown. Typically, this is a UCSC identifier like “hg19”. An attempt will be made to derive the seqinfo on the return value using either an installed BSgenome package or UCSC, if network access is available.

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 GRanges or other range-based object supported by findOverlaps. Only the intervals in the file overlapping the given ranges are returned. This is much more efficient when the file is indexed with the tabix utility.

index

If TRUE, automatically compress and index the output file with bgzf and tabix. Note that tabix indexing will sort the data by chromosome and start. Tabix supports a single track in a file.

ignore.strand

Whether to output the strand when not required (by the existence of later fields).

seqinfo

If not NULL, the Seqinfo object to set on the result. Ignored if genome is a Seqinfo object. If the genome argument is not NA, it must agree with genome(seqinfo).

extraCols

A character vector in the same form as colClasses from read.table. It should indicate the name and class of each extra/special column to read from the BED file. As BED does not encode column names, these are assumed to be the last columns in the file. This enables parsing of the various BEDX+Y formats.

sep

A character vector with a single character indicating the field separator, like read.table. This defaults to "\t", as BEDtools requires, but BED files are also allowed to be whitespace separated ("") according to the UCSC spec.

na.strings

Character vector with strings, appended to the standard ".", that represent an NA value.

append

If TRUE, and con points to a file path, the data is appended to the file. Obviously, if con is a connection, the data is always appended.

expNames

character vector naming columns in mcols(object) to export as data columns in the BED15 file. These correspond to the sample names in the experiment. If NULL (the default), there is an attempt to extract these from trackLine. If the attempt fails, no scores are exported.

...

Arguments to pass down to methods to other methods. For import, the flow eventually reaches the BEDFile method on import. When trackLine is TRUE or the target format is BED15, the arguments are passed through export.ucsc, so track line parameters are supported.

Details

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.

chrom, start, end

the ranges component.

name

character vector (NA's allowed) in the name column; defaults to NA on export.

score

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

strand factor (NA's allowed) in the strand column, accessible via the strand accessor; defaults to NA on export.

thickStart, thickEnd

IntegerRanges object in a column named thick; defaults to the ranges of the feature on export.

itemRgb

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.

blockSizes, blockStarts, blockCounts

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.

Value

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.

BEDX+Y formats

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.

BEDFile objects

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.

Author(s)

Michael Lawrence

References

Examples

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)

rtracklayer

R interface to genome annotation files and the UCSC genome browser

v1.50.0
Artistic-2.0 + file LICENSE
Authors
Michael Lawrence, Vince Carey, Robert Gentleman
Initial release

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