as_three_letter: Convert one-letter amino acid codes to three-letter codes

In grantham: Calculate the 'Grantham' Distance

Description

Converts amino acid one-letter abbreviations to three-letter codes, e.g., L to Leu. The accepted codes in the input include the 20 standard amino acids and also B (Asparagine or Aspartic acid), converted to Asx, and Z (Glutamine or Glutamic acid) converted to Glx.

Usage

as_three_letter(x)

Arguments

x	A character vector of one-letter amino acid codes, e.g. "S", "R", "L", or "P".

Value

A character vector of three-letter amino acid codes, e.g. "Ser", "Arg", "Leu", or "Pro".

Examples

# Convert S to Ser, R to Arg and P to Pro.
as_three_letter(c('S', 'R', 'P'))

# The function `as_three_letter()` is case insensitive on the input but will
# always return the three-letter codes with the first letter in uppercase.
as_three_letter(c('S', 's', 'p', 'P'))

# Convert also special case codes B (Asparagine or Aspartic acid) and Z
# (Glutamine or Glutamic acid)
as_three_letter(c('B', 'Z'))

# Invalid codes in the input are converted to NA.
# "S" is correctly mapped to "Ser" but "Ser" and "Serine" are not
# one-letter amino acid codes and are therefore converted to NA.
as_three_letter(c('S', 's', 'Ser', 'Serine'))

grantham documentation built on Jan. 7, 2022, 9:06 a.m.