bedtools_flank: bedtools_flank

In lawremi/HelloRanges: Introduce *Ranges to bedtools users

bedtools_flank

Description

Compute flanking regions.

Usage

bedtools_flank(cmd = "--help")
R_bedtools_flank(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
                 g = NULL, header = FALSE)
do_bedtools_flank(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
                  g = NULL, header = FALSE)

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.
i	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.
b	Increase the BED/GFF/VCF range by the same number base pairs in each direction. Integer.
l	The number of base pairs to subtract from the start coordinate. Integer.
r	The number of base pairs to add to the end coordinate. Integer.
s	Define l and r based on strand. For example. if used, l is 500 for a negative-stranded feature, it will add 500 bp to the end coordinate.
pct	Define l and r as a fraction of the feature length. E.g. if used on a 1000bp feature, and l is 0.50, will add 500 bp upstream..
g	Genome file, identifier or Seqinfo object that defines the order and size of the sequences.
header	Ignored.

Details

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

bedtools_flank

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

R_bedtools_flank

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

do_bedtools_flank

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

We compute the flanks with flank, although flank only computes one side at a time, so we may call it multiple times.

Value

A language object containing the compiled R code, evaluating to a GRanges object.

Author(s)

Michael Lawrence

References

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

See Also

intra-range-methods for flank.

Examples

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

## End(Not run)
## 5 on both sides
r <- bedtools_flank("-i a.bed -b 5 -g tiny.genome")
## 5 on left side
bedtools_flank("-i a.bed -l 5 -r 0 -g tiny.genome")
## define left/right in terms of transcription direction
bedtools_flank("-i a.bed -l 5 -r 0 -s -g tiny.genome")

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