seqinr: a – R documentation

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a

Converts amino-acid three-letter code into the one-letter one

Description

This is a vectorized function to convert three-letters amino-acid code into the one-letter one, for instance "Ala" into "A".

Usage

a(aa)

Arguments

`aa`	A vector of string. All strings are 3 chars long.

Details

Allowed character values for aa are given by aaa(). All other values will generate a warning and return NA. Called without arguments, a() returns the list of all possible output values.

Value

A vector of single characters.

Author(s)

D. Charif, J.R. Lobry

References

The IUPAC one-letter code for aminoacids is described at: https://www.bioinformatics.org/sms/iupac.html
citation("seqinr")

Examples

#
  # Show all possible input values:
  #
  
  aaa()
  
  #
  # Convert them in one letter-code:
  #
  
  a(aaa())
  
  #
  # Check consistency of results:
  #
  
  stopifnot( aaa(a(aaa())) == aaa())
  
  #
  # Show what happens with non-allowed values:
  #
  
  a("SOS") # should be NA and a warning is generated

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

a