amb: Expansion of IUPAC nucleotide symbols

In seqinr: Biological Sequences Retrieval and Analysis

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")

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)

seqinr documentation built on May 29, 2024, 6:36 a.m.