io-bed-read: Read a BED or BEDGraph file

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

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

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.