R/AllGenerics.R, R/Modstrings-seqtype.R
alphabet.RdThe alphabet(), shortName() fullName() and
nomenclature() functions return the letters, names and associated
abbreviations for the type of ModString. alphabet() returns the normal
letters and modification letters, whereas shortName(),
fullName() and nomenclature() return results for modifications
only.
shortName(x)
fullName(x)
nomenclature(x)
# S4 method for class 'ModString'
alphabet(x, baseOnly = FALSE)
# S4 method for class 'ModStringSet'
alphabet(x, baseOnly = FALSE)
# S4 method for class 'ModString'
shortName(x)
# S4 method for class 'ModStringSet'
shortName(x)
# S4 method for class 'ModString'
fullName(x)
# S4 method for class 'ModStringSet'
fullName(x)
# S4 method for class 'ModString'
nomenclature(x)
# S4 method for class 'ModStringSet'
nomenclature(x)a character vector.
alphabet(ModDNAString())
#> [1] "A" "C" "G" "T" "N" "-" "+" "." "p" "δ" "O" "]" "D" "J" "e"
#> [16] "g" "`" "b" "U" "∝" "π" "I" "7" "6" "3" "2" "1" "8" "∉" "⊆"
#> [31] "⊇" "R" "α" "m" "h" "×" "f" "4" "ν" "X" "'" "κ" "o" "(" ")"
#> [46] "η" "a" "⇓" "⇑" "\"" "√" "/" "≡" "ζ" "~"
shortName(ModDNAString())
#> [1] "5pT" "3mT" "O4meT" "1mT" "dhT" "baseJ" "5fU" "5hmU"
#> [9] "dhpU" "5caU" "dU" "DHdU" "5nmU" "dI" "7mG" "6mG"
#> [17] "3mG" "2mG" "1mG" "8oxoG" "7a7dG" "12eG" "23eG" "2,2mG"
#> [25] "2ceG" "5mC" "5hmC" "5gmC" "5fC" "5caC" "4mC" "34eC"
#> [33] "3mC" "3eC" "2mC" "1mC" "9mA" "7mA" "6mA" "4mA"
#> [41] "3mA" "1mA" "6haA" "2mA" "2a6haA" "6,6mA" "6ncmA"
nomenclature(ModDNAString())
#> [1] "5pT" "3mT" "O4meT" "1mT" "dhT" "baseJ" "5fU" "5hmU"
#> [9] "dhpU" "5caU" "dU" "DHdU" "5nmU" "dI" "7mG" "6mG"
#> [17] "3mG" "2mG" "1mG" "8oxoG" "7a7dG" "12eG" "23eG" "2,2mG"
#> [25] "2ceG" "5mC" "5hmC" "5gmC" "5fC" "5caC" "4mC" "34eC"
#> [33] "3mC" "3eC" "2mC" "1mC" "9mA" "7mA" "6mA" "4mA"
#> [41] "3mA" "1mA" "6haA" "2mA" "2a6haA" "6,6mA" "6ncmA"