seqinr: amb – R documentation

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amb

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: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/

citation("seqinr")

Examples

#
# The list of IUPAC symbols:
#

amb()

#
# And their expansion:
#

sapply(amb(), amb)

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19

amb