R: Computing an IUPAC nucleotide symbol

bma {seqinr} | R Documentation

## Computing an IUPAC nucleotide symbol

### Description

This function returns the IUPAC symbol for a nucleotide sequence, for instance `c("c", "c", "g")` is coded by `"s"`.

### Usage

    bma(nucl, warn.non.IUPAC = TRUE, type = c("DNA", "RNA"))

### Arguments

`nucl` | a nucleotide sequence as a vector of single chars
`warn.non.IUPAC` | if TRUE warns when no IUPAC symbol is possible
`type` | whether this is a DNA or a RNA sequence

### Details

The sequence is forced in lower case letters and ambiguous bases are expanded before trying to find an IUPAC symbol.

### Value

A single IUPAC symbol in lower case, or NA when this is not possible.

### Author(s)

J.R. Lobry

### References

The nomenclature for incompletely specified bases in nucleic acid sequences at: http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html

`citation("seqinr")`

### See Also

See `amb` for the reverse operation. Use `toupper` to change lower case letters into upper case letters.

### Examples

    stopifnot(bma(s2c("atatattttata")) == "w")
    stopifnot(bma(s2c("gcggcgcgcggc")) == "s")
    stopifnot(bma(s2c("ACGT")) == "n")
    stopifnot(is.na(bma(s2c("atatttt---tatat")))) # a warning is issued

[Package seqinr version 3.4-5 Index]