bedtools_multiinter {HelloRanges} | R Documentation

## 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")

[Package HelloRanges version 1.13.0 Index]