io-bed-write: Write a BED or BEDGraph file

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

Write a BED or BEDGraph file

Description

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

Usage

write_bed(x, file, index = FALSE)

write_bed_graph(x, file, index = FALSE)

write_narrowpeaks(x, file)

Arguments

x	A GRanges object
file	File name, URL or connection specifying a file to write x to. Compressed files with extensions such as '.gz' are handled automatically. If you want to index the file with tabix use the index argument.
index	Compress and index the output file with bgzf and tabix (default = FALSE). Note that tabix indexing will sort the data by chromosome and start.

Value

The write functions return a BED(Graph)File invisibly

See Also

rtracklayer::BEDFile()

Examples

## Not run: 
  test_path <- system.file("tests", package = "rtracklayer")
  bed_file <- file.path(test_path, "test.bed")
  gr <- read_bed(bed_file)
  bed_file_out <- file.path(tempdir(), "new.bed")
  write_bed(gr, bed_file_out)
  read_bed(bed_file_out)
  #' bedgraph
  bg_file <- file.path(test_path, "test.bedGraph")
  gr <- read_bed_graph(bg_file)
  bg_file_out <- file.path(tempdir(), "new.bg")
  write_bed(gr, bg_file_out)
  read_bed(bg_file_out)
  # narrowpeaks
  np_file <- system.file("extdata", "demo.narrowPeak.gz",package="rtracklayer")
  gr <- read_narrowpeaks(np_file, genome_info = "hg19")
  np_file_out <- file.path(tempdir(), "new.bg")
  write_narrowpeaks(gr, np_file_out)
  read_narrowpeaks(np_file_out)

## End(Not run)

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