substitution_mutator: Perform substitution mutations on a nucelotide sequence.

In zcolburn/evolution: Genetic Algorithm For Protein Engineering

Description

Perform substitution mutations on a nucelotide sequence.

Usage

substitution_mutator(nt_sequence, sub_rate_A_to_T = 0.05,
  sub_rate_A_to_C = 0.05, sub_rate_A_to_G = 0.05, sub_rate_T_to_A = 0.05,
  sub_rate_T_to_C = 0.05, sub_rate_T_to_G = 0.05, sub_rate_C_to_A = 0.05,
  sub_rate_C_to_T = 0.05, sub_rate_C_to_G = 0.05, sub_rate_G_to_A = 0.05,
  sub_rate_G_to_T = 0.05, sub_rate_G_to_C = 0.05)

Arguments

nt_sequence	A vector of nucleotides, i.e. c("C","A","T","G","A").
sub_rate_A_to_T	The probability of an "A" becoming a "T".
sub_rate_A_to_C	The probability of an "A" becoming a "C".
sub_rate_A_to_G	The probability of an "A" becoming a "G".
sub_rate_T_to_A	The probability of an "T" becoming a "A".
sub_rate_T_to_C	The probability of an "T" becoming a "C".
sub_rate_T_to_G	The probability of an "T" becoming a "G".
sub_rate_C_to_A	The probability of an "C" becoming a "A".
sub_rate_C_to_T	The probability of an "C" becoming a "T".
sub_rate_C_to_G	The probability of an "C" becoming a "G".
sub_rate_G_to_A	The probability of an "G" becoming a "A".
sub_rate_G_to_T	The probability of an "G" becoming a "T".
sub_rate_G_to_C	The probability of an "G" becoming a "C".

Details

Pass in a vector of nucleotides and the probability of each type of substitution mutation. Get back a mutated vector.

Value

A vector of nucleotides, i.e. c("C","A","A","G","A"), with subsitution mutations included.

Examples

set.seed(1)
substitution_mutator(
c("C","A","T","G","A")
)

zcolburn/evolution documentation built on May 19, 2019, 1:48 a.m.