select_alternative: select_alternative

In ec363/synonymise: Generate synonymous CDS of frequently used protein motifs, keep DNA synthesis companies happy!

Description

Select a codon from a provided list that has a decent codon usage. Works by selecting a codon at random from the possible_codons list until it isn't also on the excluded forbidden_codons list. Codon lists with only one variant, or with no non-forbidden options will return original codon. Returned codon is provided as lower case string. Verbose option helps to follow the function as it is working. Is called by synonymise function, but can also be used independently.

Usage

select_alternative(input = "", possible_codons, forbidden_codons,
  verbose = FALSE)

Arguments

input	optional. string used to specify input codon, only required for verbosity. Defaults to "".
possible_codons	dataframe of codons to choose from (eg. output from find_synonymous_codons function).
forbidden_codons	dataframe of codons to exclude, such as rare codons.
verbose	logical. Defaults to FALSE.

Examples

select_alternative(possible_codons = synonymous_codons, forbidden_codons = c(very_rare_codons, rare_codons), verbose=TRUE, input="CGC")

ec363/synonymise documentation built on Aug. 9, 2020, 1:34 a.m.