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Calculate Q matrix from nucleotide substitution rates

Source: R/estimate_q.R
calc_q_from_rates.Rd

Method:

  • If needed, convert rates per day to rates per generation

  • Convert rates per generation to probabilities per generation

  • Make diagonal such that rows of probability matrix p sum to 1

  • Convert to q matrix, assuming a mutation rate of mut_rate mutations/site/generation, by solving for q in the equation p = exp(q*mut_rate)

Usage

calc_q_from_rates(rates, mut_rate, generation_time = NULL)

Arguments

rates

4x4 matrix of individual nucleotide substitution rates for each potential substitution (per-site per-generation or per-site per-day) with the following row and column names: A,C,G,T.

mut_rate

Overall per-site per-generation mutation rate.

generation_time

Generation time (if nucleotide substitution rates are in days rather than generations; default: NULL, assumes that rate matrix is per-generation)

Value

Nucletoide substitution rate matrix Q

Examples

calc_q_from_rates(hiv_mut_rates, 2.4e-5, 1.2)
#>            A          C          G          T
#> A -1.3935602  0.1650215  1.1002145  0.1283242
#> C  0.9167813 -3.2089352  0.0915972  2.2005567
#> G  2.9338881  0.0182889 -3.3189236  0.3667466
#> T  0.5499598  1.8338005  0.5501132 -2.9338736