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

Description Usage Arguments Details Value See Also Examples

Description

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

Read common interval based formats as GRanges.

Usage

1
2
3
4
5
6
7
8
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):

Value

A GRanges object

See Also

rtracklayer::BEDFile()

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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

plyranges documentation built on Nov. 1, 2018, 3:58 a.m.