R: Expansion of IUPAC nucleotide symbols

amb {seqinr} | R Documentation

## Expansion of IUPAC nucleotide symbols

### Description

This function returns the list of nucleotide matching a given IUPAC nucleotide symbol, for instance `c("c", "g")` for `"s"`.

### Usage

    amb(base, forceToLower = TRUE, checkBase = TRUE,
    IUPAC = s2c("acgturymkswbdhvn"), u2t = TRUE)

### Arguments

`base` | an IUPAC symbol for a nucleotide as a single character
`forceToLower` | if TRUE the base is forced to lower case
`checkBase` | if TRUE the character is checked to belong to the allowed IUPAC symbol list
`IUPAC` | the list of allowed IUPAC symbols
`u2t` | if TRUE "u" for uracil in RNA are changed into "t" for thymine in DNA

### Details

Non ambiguous bases are returned unchanged (except for "u" when u2t is TRUE).

### Value

When base is missing, the list of IUPAC symbols is returned, otherwise a vector with expanded symbols.

### 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 `bma` for the reverse operation. Use `tolower` to change upper case letters into lower case letters.

### Examples

    #
    # The list of IUPAC symbols:
    #

    amb()

    #
    # And their expansion:
    #

    sapply(amb(), amb)

[Package seqinr version 3.4-5 Index]