read_bed {plyranges} | R Documentation

## Read a BED or BEDGraph file

### Description

This is a lightweight wrapper to the import family of functions defined in rtracklayer.

Read common interval based formats as GRanges.

### Usage

    read_bed(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

    read_bed_graph(
      file,
      col_names = NULL,
      genome_info = NULL,
      overlap_ranges = NULL
    )

    read_narrowpeaks(
      file,
      col_names = NULL,
      genome_info = NULL,
      overlap_ranges = NULL
    )

### Arguments

`file` | A path to a file or a connection.
`col_names` | An optional character vector for including additional columns in `file` that are not part of the BED/narrowPeaks specification.
`genome_info` | An optional character string or a Ranges object that contains information about the genome build. For example the USSC identifier "hg19" will add build information to the returned GRanges.
`overlap_ranges` | An optional Ranges object. Only the intervals in the file that overlap the Ranges will be returned.

### Details

This is a lightweight wrapper to the import family of functions defined in rtracklayer. The `read_narrowpeaks` function parses the ENCODE narrowPeak BED format (see https://genome.ucsc.edu/FAQ/FAQformat.html#format12 for details.). As such the parser expects four additional columns called (corresponding to the narrowPeaks spec):

- signalValue

- pValue

- qValue

- peak

### Value

A GRanges object

### See Also

`rtracklayer::BEDFile()`

### Examples

    test_path <- system.file("tests", package = "rtracklayer")
    bed_file <- file.path(test_path, "test.bed")
    gr <- read_bed(bed_file)
    gr
    gr <- read_bed(bed_file, genome_info = "hg19")
    gr
    olap <-  as_granges(data.frame(seqnames = "chr7", start = 1, end = 127473000))
    gr <- read_bed(bed_file,
                  overlap_ranges = olap)
    # bedGraph
    bg_file <- file.path(test_path, "test.bedGraph")
    gr <- read_bed_graph(bg_file)
    gr
    # narrowpeaks
    np_file <- system.file("extdata", "demo.narrowPeak.gz",  package="rtracklayer")
    gr <- read_narrowpeaks(np_file, genome_info = "hg19")
    gr

[Package plyranges version 1.12.1 Index]