write_bed {plyranges} | R Documentation

## 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)

[Package plyranges version 1.12.1 Index]