bedtools_merge {HelloRanges} | R Documentation

## bedtools_merge

### Description

Collapse overlapping and adjacent ranges into a single range, i.e., `reduce` the ranges. Then, group the original ranges by reduced range and aggregate. By default, the scores are summed.

### Usage

    bedtools_merge(cmd = "--help")
    R_bedtools_merge(i, s = FALSE, S = c("any", "+", "-"), d = 0L, c = NULL,
                     o = "sum", delim = ",")
    do_bedtools_merge(i, s = FALSE, S = c("any", "+", "-"), d = 0L, c = NULL,
                      o = "sum", delim = ",")

### 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. These are the ranges that are merged.
`s` | Require same strandedness. That is, find the jaccard 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` | Force merge for one specific strand only. Follow with + or - to force merge from only the forward or reverse strand, respectively. By default, merging is done without respect to strand.
`d` | Maximum distance between features allowed for features to be merged. Default is 0. That is, overlapping and/or book-ended features are merged.
`c` | Specify columns (by integer index) from the input file to operate upon (see `o` option, below). Multiple columns can be specified in a comma-delimited list.
`o` | Specify the operations (by name) that should be applied to the columns indicated in `c`. Multiple operations can be specified in a comma-delimited list. Recycling is used to align `c` and `o`. See `bedtools_groupby` for the available operations. Defaults to the “sum” operation.
`delim` | Delimiter character used to collapse strings.

### Details

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

`bedtools_merge`

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

`R_bedtools_merge`

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

`do_bedtools_merge`

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

The workhorse for reduction is `reduce`. Passing `with.revmap=TRUE` to `reduce` causes it to return a list of integers, which can be passed directly to `aggregate` to aggregate the original ranges.

Since the grouping information is preserved in the result, this function serves as a proxy for `bedtools cluster`.

### Value

A language object containing the compiled R code, evaluating to a DataFrame with a “grouping” column corresponding to `as(hits, "List")`, and a column for each summary.

### Author(s)

Michael Lawrence

### References

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

### See Also

bedtools_groupby for more details on bedtools-style aggregation, reduce for merging, aggregate-methods for aggregating.

### Examples

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

    ## End(Not run)
    ## default behavior, sum the score
    bedtools_merge("-i a.bed")
    ## count the seqnames
    bedtools_merge("-i a.bed -c 1 -o count")
    ## collapse the names using "|" as the delimiter
    bedtools_merge("-i a.names.bed -delim \"|\" -c 4  -o collapse")
    ## collapse the names and sum the scores
    bedtools_merge("-i a.full.bed -c 4,5  -o collapse,sum")
    ## count and sum the scores
    bedtools_merge("-i a.full.bed -c 5  -o count,sum")
    ## only merge the positive strand features
    bedtools_merge("-i a.full.bed -S +")

[Package HelloRanges version 1.13.0 Index]