Deviation from Proportionality — get

get_dp calculates Deviation from Proportionality of each CDS.

Usage

get_dp(
  cf,
  host_weights,
  codon_table = get_codon_table(),
  level = "subfam",
  missing_action = "ignore"
)

Arguments

cf: matrix of codon frequencies as calculated by count_codons().
host_weights: a named vector of tRNA weights for each codon that reflects the relative availability of tRNAs in the host organism.
codon_table: a table of genetic code derived from get_codon_table or create_codon_table.
level: "subfam" (default) or "amino_acid". If "subfam", the deviation is calculated at the codon subfamily level. Otherwise, the deviation is calculated at the amino acid level.
missing_action: Actions to take when no codon of a group were found in a CDS. Options are "ignore" (default), or "zero" (set codon proportions to 0).

Value

a named vector of dp values.

References

Chen F, Wu P, Deng S, Zhang H, Hou Y, Hu Z, Zhang J, Chen X, Yang JR. 2020. Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection. Nat Ecol Evol 4:589-600.

Examples

# estimate DP of yeast genes
cf_all <- count_codons(yeast_cds)
trna_weight <- est_trna_weight(yeast_trna_gcn)
trna_weight <- setNames(trna_weight$w, trna_weight$codon)
dp <- get_dp(cf_all, host_weights = trna_weight)
head(dp)
#>   YPL071C   YLL050C   YMR172W   YOR185C   YLL032C   YBR225W 
#> 0.3994734 0.3997561 0.2949640 0.3086534 0.3079175 0.3265945 
hist(dp)