codon_replacement {immuneSIM}

Replaces codons with synonymous codons

Description

Replaces codons with synonymous codons

Usage

codon_replacement(repertoire, mode = "both", codon_replacement_list,
  skip_probability = 0)

Arguments

repertoire

An annotated AIRR compliant immuneSIM repertoire.

(http://docs.airr-community.org/en/latest/)

mode

Defines whether codons should be replaced in the nt or AA sequence or in both ("nt","AA","both")

codon_replacement_list

List containing instructions for which codons should be replaced and how

skip_probability

Probability with which a sequence gets skipped in the codon replacement process between 0,1

Value

immuneSIM repertoire with replaced codons

Examples

repertoire <- list_example_repertoires[["example_repertoire_A"]]
rep_codon_repl <- codon_replacement(repertoire, "both",
list(tat = "tac", agt = "agc", gtt = "gtg"), 0)