rrt: Random reverse translation

Description Usage Arguments Value

View source: R/rrt.r

Description

Randomly reverse translate an animo acid sequence into a DNA sequence according to a codon usage table and a codon table

Usage

1
rrt(x, cut, y = 0, spp)

Arguments

x

a char array of animo acids (e.g., either 'G' or 'Gly' is acceptable but do not mix one letter symbols with three letter symbols in the same array) or codons (e.g., 'GGG'). The first element of the array will be used to determine the type of the input

cut

a named numerical array of codon usage table. Case-insensitive three letter codon names are used. Numbers could be the actuall codon counts or scaled ratios

y

a number denoting the codon table to be used. When cut is specified, y also needs to be specified. 0 = standard codon table (default), 2 = vertibrate mitchodrial and see dna2aa for more options. When an option other than those mentioned above is provided, the standard codon table will be used

spp

a char string of the host species name for which the codon usage table will be used: 'ecoli', E. coli; 'insect', insect; 'yeast', yeast; 'celegans', C. elegans, and see pminmax for more options. When specified, this option overides cut. These build-in codon usage tables are taken from https://www.genscript.com/tools/codon-frequency-table.

Value

an KZsqns object of random reverse translated codons


HVoltBb/kondonz documentation built on Jan. 11, 2020, 3:30 a.m.