bedtools_multiinter: bedtools_multiinter

In lawremi/HelloRanges: Introduce *Ranges to bedtools users

bedtools_multiinter

Description

Summarize the ranges according to disjoin and annotate each disjoint range with the samples that overlap the range.

Usage

bedtools_multiinter(cmd = "--help")
R_bedtools_multiinter(i, header=FALSE, names=NULL, g=NA_character_,
                      empty=FALSE)
do_bedtools_multiinter(i, header=FALSE, names=NULL, g=NA_character_,
                       empty=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	Paths to BAM/BED/GFF/VCF/etc files (vector or comma-separated), or a list of objects.
header	Ignored.
names	Provide an alias for each to use for each i instead of their integer index. If a single string, can be comma-separated.
g	A genome file, identifier or Seqinfo object that defines the order and size of the sequences.
empty	Report empty regions (i.e., regions not covered in any of the files). This essentially yields a partitioning of the genome (and thus requires g to be specified).

Details

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

bedtools_multiinter

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

R_bedtools_multiinter

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

do_bedtools_multiinter

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

The workhorse is disjoin. Passing with.revmap=TRUE to disjoin causes it to return a list of integers, which we use to extract the sample identifiers. The empty case requires a bit more code, because we have to combine the disjoint ranges with the gaps.

Value

A language object containing the compiled R code, evaluating to a GRanges with a column “i” indicating the sample memberships.

Author(s)

Michael Lawrence

References

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

See Also

disjoin for forming disjoint ranges.

Examples

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

## End(Not run)
## default behavior
bedtools_multiinter("-i a.bed,b.bed,c.bed")
## custom names
bedtools_multiinter("-i a.bed,b.bed,c.bed -names A,B,C")
## include empty regions, i.e., partition the genome
bedtools_multiinter("-i a.bed,b.bed,c.bed -names A,B,C -empty -g test.genome")

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