Estimate Amino Acid Usage Frequencies of CDSs.
Usage
est_aau(cf, codon_table = get_codon_table())Value
a data.table with amino acid frequencies of CDSs. The columns include three-letter abbreviation of the amino acid, single-letter abbreviation, usage frequency of the amino acid in all sequences, and usage frequency proportion.
Examples
# estimate amino acid frequencies of yeast genes
cf_all <- count_codons(yeast_cds)
aau <- est_aau(cf_all)
print(aau)
#> amino_acid aa_code count proportion
#> <char> <char> <num> <num>
#> 1: Phe F 133094 0.04567496
#> 2: Leu L 281010 0.09643651
#> 3: Ser S 263057 0.09027543
#> 4: Tyr Y 97696 0.03352714
#> 5: Cys C 38839 0.01332870
#> 6: Trp W 30566 0.01048958
#> 7: Pro P 125783 0.04316598
#> 8: His H 62347 0.02139613
#> 9: Gln Q 113195 0.03884606
#> 10: Arg R 130244 0.04469690
#> 11: Ile I 191381 0.06567779
#> 12: Met M 61057 0.02095343
#> 13: Thr T 170219 0.05841545
#> 14: Asn N 176635 0.06061728
#> 15: Lys K 212102 0.07278878
#> 16: Val V 163969 0.05627059
#> 17: Ala A 160384 0.05504029
#> 18: Asp D 167835 0.05759731
#> 19: Glu E 188978 0.06485313
#> 20: Gly G 145547 0.04994856
#> amino_acid aa_code count proportion