bedtools_subtract {HelloRanges} | R Documentation

## bedtools_subtract

### Description

Subtracts one set of ranges from another, either by position or range.

### Usage

    bedtools_subtract(cmd = "--help")
    R_bedtools_subtract(a, b, f = 1e-09, F = 1e-09, r = FALSE, e = FALSE,
                        s = FALSE, S = FALSE, A = FALSE, N = FALSE,
                        g = NA_character_)
    do_bedtools_subtract(a, b, f = 1e-09, F = 1e-09, r = FALSE, e = FALSE,
                         s = FALSE, S = FALSE, A = FALSE, N = FALSE,
                         g = NA_character_)

### 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.
`a` | Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or a ranged data structure, such as a GRanges. Each feature in `a` is compared to `b` in search of overlaps. 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` | Like `a`, except supports multiple datasets, either as a vector/list or a comma-separated string. Also supports file glob patterns, i.e., strings containing the wildcard, “*”.
`f` | Minimum overlap required as a fraction of `a` [default: any overlap].
`F` | Minimum overlap required as a fraction of `b` [default: any overlap].
`r` | Require that the fraction of overlap be reciprocal for `a` and `b`. In other words, if `f` is 0.90 and `r` is `TRUE`, this requires that `b` overlap at least 90% of `a` and that `a` also overlaps at least 90% of `b`.
`e` | Require that the minimum fraction be satisfied for `a` OR `b`. In other words, if `e` is `TRUE` with `f=0.90` and `F=0.10` this requires that either 90% of `a` is covered OR 10% of `b` is covered. If `FALSE`, both fractions would have to be satisfied.
`s` | Require same strandedness. That is, find the subtract feature in `b` that overlaps `a` on the same strand. By default, overlaps are reported without respect to strand. Note that this is the exact opposite of Bioconductor behavior.
`S` | Require opposite strandedness. That is, find the subtract feature in `b` that overlaps `a` on the opposite strand. By default, overlaps are reported without respect to strand.
`A` | Remove entire feature if any overlap. If a feature in `a` overlaps one in `b`, the entire feature is removed.
`N` | Same as `A=TRUE` except when considering `f` the numerator in the fraction is the sum of the overlap for all overlapping features in `b`.
`g` | A genome file, identifier or Seqinfo object that defines the order and size of the sequences.

### Details

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

`bedtools_subtract`

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

`R_bedtools_subtract`

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

`do_bedtools_subtract`

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

We typically subtract sets of ranges using `setdiff`; however, that will not work here, because we cannot merge the ranges in `a`.

The algorithm has two modes: by position (where ranges are clipped) and by range (where ranges are discarded entirely). The position mode is the default. We find overlaps, optionally restrict them, and for each range in `a`, we subtract all of the qualifying intersections in `b`.

When `A` or `N` are `TRUE`, we use the second mode. In the simplest case, that is just `subsetByOverlaps` with `invert=TRUE`, but fractional overlap restrictions and `N` make that more complicated.

### Value

A language object containing the compiled R code, evaluating to a GRanges object, except when `A` or `N` are `TRUE`, where the value might be a GRanges, GAlignments or VCF object, depending on the input.

### Author(s)

Michael Lawrence

### References

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

### See Also

setops-methods for set operations including setdiff, findOverlaps-methods for different ways to detect overlaps.

### Examples

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

    ## End(Not run)

    ## simple case, position-wise subtraction
    bedtools_subtract("-a a.bed -b b.bed")
    ## fractional overlap restriction
    bedtools_subtract("-a a.bed -b b.bed -f 0.5")
    ## range-wise subtraction
    bedtools_subtract("-a a.bed -b b.bed -A -f 0.5")

[Package HelloRanges version 1.16.0 Index]