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.
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")
#> P2S
#> P2R
#> P2L
#> P2T
#> P2A
#> P2V
#> P2G
#> P2I
#> P2F
#> P2Y
#> P2C
#> P2H
#> P2Q
#> P2N
#> P2K
#> P2D
#> P2E
#> P2M
#> P2W
#>
read_substitutions(file = my_file)
#> # A tibble: 19 × 4
#> res poi ref sub
#> <int> <int> <chr> <chr>
#> 1 2 NA P S
#> 2 2 NA P R
#> 3 2 NA P L
#> 4 2 NA P T
#> 5 2 NA P A
#> 6 2 NA P V
#> 7 2 NA P G
#> 8 2 NA P I
#> 9 2 NA P F
#> 10 2 NA P Y
#> 11 2 NA P C
#> 12 2 NA P H
#> 13 2 NA P Q
#> 14 2 NA P N
#> 15 2 NA P K
#> 16 2 NA P D
#> 17 2 NA P E
#> 18 2 NA P M
#> 19 2 NA P W
# 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"))
#> # A tibble: 117 × 4
#> res poi ref sub
#> <int> <int> <chr> <chr>
#> 1 1647 NA N K
#> 2 1651 NA S F
#> 3 1652 NA M T
#> 4 1652 NA M I
#> 5 1653 NA V M
#> 6 1655 NA S F
#> 7 1656 NA G D
#> 8 1662 NA F S
#> 9 1663 NA M L
#> 10 1663 NA M K
#> # ℹ 107 more rows