genCode-class {coRdon} | R Documentation |
genCode
Object of genCode
class describes the variant of genetic code
to be used in CU calculations.
genCode(id_or_name2 = "1", alt.init = TRUE, stop.rm = FALSE) ## S4 method for signature 'ANY' genCode(id_or_name2 = "1", alt.init = TRUE, stop.rm = FALSE)
id_or_name2 |
A single string that uniquely identifies the genetic code to extract.
Should be one of the values in the |
alt.init |
logical, whether to use alternative initiation codons.
Default is |
stop.rm |
logical, whether to remove stop codons. Default is
|
A genCode
object.
genCode
: Creates new instances of genCode
class.
ctab
A data.table
with two colums:
codon
and AA
, amino acid.
codons
A character vector of codons.
stops
A character vector of stop codons. Note that,
if stop.rm
is TRUE
, this will be
an empty vector.
nostops
A character vector of no-stop codons.
If stop.rm
is TRUE
, this will be
equal to the codons
slot.
cl
A list, each element of which is a vector of integers indicating the positions of synonymous codons for that amino acid, when codons are ordered alphabetically.
deg
A numeric vector of degeneracies for alphabetically ordered amino acids.