read_substitutions: Read a file with amino acid substitutions

In agvgd: An R Implementation of the 'Align-GVGD' Method

Read a file with amino acid substitutions

Description

This function reads a file with amino acid substitutions. The format of should be the same one as requested by the web version of Align-GVGD.

Usage

read_substitutions(
  file = stop("`file` must be specified"),
  amino_acid_code = c("one_letter", "three_letter")
)

Arguments

file	The path to a file with amino acid substitutions.
amino_acid_code	The type of symbol used for amino acids in the returned output.

Value

A tibble listing the amino acids substitutions.

Examples

# "sub.txt" is an example file containing missense substitutions formatted
# according to the requirements indicated in http://agvgd.hci.utah.edu/help.php.
my_file <- system.file("extdata", "sub.txt", package = "agvgd")
cat(readLines(my_file), sep = "\n")

read_substitutions(file = my_file)

# lee2010_sub.txt is a file containing the missense variants studied by
# Lee et al. (2010): https://doi.org/10.1158/0008-5472.CAN-09-4563.
read_substitutions(file = system.file("extdata", "lee2010_sub.txt", package = "agvgd"))

agvgd documentation built on Sept. 11, 2022, 1:07 a.m.