Base information for sequence characters of nucleotide strings containing modifications

The 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)

Arguments

x

a ModString or ModStringSet object

baseOnly

TRUE or FALSE (default): Should the result omit occurances of the letters N.-+?

Value

a character vector.

Examples

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"