seqinr (version 4.2-30)

bma: 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"))

Value

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

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

Author

J.R. Lobry

Details

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

References

The nomenclature for incompletely specified bases in nucleic acid sequences at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/

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