bedtools_nuc {HelloRanges} | R Documentation

## bedtools_nuc

### Description

Summarize DNA sequences over the specified ranges.

### Usage

        bedtools_nuc(cmd = "--help")
        R_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = FALSE)
        do_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = 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.
`fi` | Path to a FASTA file, or an XStringSet.
`bed` | Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or a ranged data structure, such as a GRanges, as the query. 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.
`s` | Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented.
`pattern` | Optional sequence pattern to count in each subsequence.
`fullHeader` | Use the full FASTA header as the names. By default, use just the first word.

### Details

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

`bedtools_nuc`

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

`R_bedtools_nuc`

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

`do_bedtools_nuc`

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

Computes AT/GC percentage and counts each type of base. Relies on Biostrings utilities like `letterFrequency` and `alphabetFrequency`. The counting of `pattern` occurrences uses `vcountPattern`.

### Value

A language object containing the compiled R code, evaluating to a DataFrame with summary statistics including the AC and GT percentage, and the counts of each type of base. Also includes the count of `pattern`, if specified.

### Author(s)

Michael Lawrence

### References

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

### See Also

letterFrequency for summarizing sequences, matchPattern for pattern matching.

### Examples

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

    ## End(Not run)
        ## default behavior, note the two dashes in '--fi'
        bedtools_nuc("--fi test.fasta -bed a.bed")
        ## with pattern counting
        bedtools_nuc("--fi test.fasta -bed a.bed -pattern ATA")

[Package HelloRanges version 1.13.0 Index]