bedtools_groupby {HelloRanges} | R Documentation

## bedtools_groupby

### Description

Query sequence from a FASTA file given a set of ranges, including compound regions like transcripts and junction reads. This assumes the sequence is DNA.

### Usage

        bedtools_groupby(cmd = "--help")
        R_bedtools_groupby(i, g = 1:3, c, o = "sum", delim=",")
        do_bedtools_groupby(i, g = 1:3, c, 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.
`g` | Column index(es) for grouping the input. Columns may be comma-separated. By default, the grouping is by range.
`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 the details for the available operations.
`delim` | Delimiter character used to collapse strings.

### Details

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

`bedtools_groupby`

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

`R_bedtools_groupby`

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

`do_bedtools_groupby`

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

The workhorse for aggregation in R is `aggregate` and we have extended its interface to make it more convenient. See `aggregate` for details.

The following operations are supported (with R translation):

sum

  `sum(X)`

min

  `min(X)`

max

  `max(X)`

absmin

  `min(abs(X))`

absmax

  `max(abs(X))`

mean

  `mean(X)`

median

  `median(X)`

mode

  `distmode(X)`

antimode

  `distmode(X, anti=TRUE)`

collapse

  `unstrsplit(X, delim)`

distinct

  `unstrsplit(unique(X), delim)`

count

  `lengths(X)`

count_distinct

  `lengths(unique(X))`

sstdev

  `sd(X)`

`freq` `table(X)` `first` `drop(heads(X, 1L))` `last` `drop(tails(X, 1L))`

For the sake of simplicity, and because the use cases are not clear, we do not support aggregation of every column. Here are some of the restrictions:

- No support for the last column of GFF (the ragged list of attributes).

- No support for the INFO, FORMAT and GENO fields of VCF.

- No support for the FLAG field of BAM (`bedtools` does not support this either).

### Value

A language object containing the compiled R code, generally evaluating to a DataFrame, with a column for each grouping variable and each summarized variable. As a special case, if there are no grouping variables specified, then the grouping is by range, and an aggregated GRanges is returned.

### Note

We admit that using column subscripts for `c` makes code hard to read. All the more reason to just write R code.

### Author(s)

Michael Lawrence

### References

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

### See Also

`aggregate-methods` for general aggregation.

### Examples

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

    ## End(Not run)
        ## aggregation by range
        bedtools_groupby("-i values3.header.bed -c 5")
        ## average variant qualities by chromosome and reference base
    ## Not run:
        indexTabix(bgzip("a_vcfSVtest.vcf", overwrite=TRUE), "vcf")

    ## End(Not run)
        bedtools_groupby("-i a_vcfSVtest.vcf.bgz -g 1,4 -c 6 -o mean")

[Package HelloRanges version 1.10.0 Index]