cubar (version 1.2.0)

get_dp: Deviation from Proportionality

Description

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"
)

Value

a named vector of dp values. The names of the elements correspond to the sequence names.

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).

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)
hist(dp)