bedtools_makewindows: bedtools_makewindows

In lawremi/HelloRanges: Introduce *Ranges to bedtools users

bedtools_makewindows

Description

Generate a partitioning/tiling or set of sliding windows over the genome or a set of ranges.

Usage

bedtools_makewindows(cmd = "--help")
R_bedtools_makewindows(b, g = NA_character_, w, s, n)
do_bedtools_makewindows(b, g = NA_character_, w, s, n)

Arguments

cmd	String of bedtools command line arguments, as they would be entered at the shell. There are a few incompatibilities between the docopt parser and the bedtools style. See argument parsing.
b	Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or a ranged data structure, such as a GRanges. Use "stdin" for input from another process (presumably while running via Rscript). For streaming from a subprocess, prefix the command string with “<”, e.g., "<grep foo file.bed". Any streamed data is assumed to be in BED format. Windows are generated with each range. Exclusive with g.
g	A genome file, identifier or Seqinfo object that defines the order and size of the sequences. Specifying this generates windows over the genome. Exclusive with b.
w	Window size, exclusive with n.
s	Step size (generates sliding windows).
n	Number of windows, exclusive with w.

Details

As with all commands, there are three interfaces to the makewindows command:

bedtools_makewindows

Parses the bedtools command line and compiles it to the equivalent R code.

R_bedtools_makewindows

Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.

do_bedtools_makewindows

Evaluates the result of R_bedtools_makewindows. Recommended only for demonstration and testing. It is best to integrate the compiled code into an R script, after studying it.

We view the generation of a partitioning (or tiling) as a distinct use case from the generation of sliding windows. The two use cases correspond to the tile and slidingWindows functions, respectively.

Value

A language object containing the compiled R code, evaluating to a a GRangesList containing the windows for each range (or chromosome).

Author(s)

Michael Lawrence

References

http://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html

See Also

tile-methods for generating windows.

Examples

## Not run: 
setwd(system.file("unitTests", "data", "makewindows", package="HelloRanges"))

## End(Not run)

## tiles of width 5000
bedtools_makewindows("-b input.bed -w 5000")
## sliding windows, 5kb wide, every 2kb
bedtools_makewindows("-b input.bed -w 5000 -s 2000")
## 3 tiles in each range
bedtools_makewindows("-b input.bed -n 3")
## 3 tiles for each chromosome of the genome
bedtools_makewindows("-g test.genome -n 3")

lawremi/HelloRanges documentation built on Oct. 29, 2023, 4:08 p.m.