extract_trna_gcn | R Documentation |
extract_trna_gcn
processes tRNA sequence data from GtRNADB to
extract gene copy numbers for each tRNA type. This information is essential
for calculating tRNA availability weights used in TAI analysis.
extract_trna_gcn(trna_seq)
trna_seq |
A named vector or DNAStringSet of tRNA sequences, typically from GtRNADB. Sequence names should follow the standard format containing amino acid and anticodon information (e.g., "tRNA-Ala-AGC-1-1"). |
A named table of tRNA gene copy numbers. Names are in the format "AminoAcid-Anticodon" (e.g., "Ala-AGC") and values represent the count of genes encoding each tRNA type. Initiator tRNAs (iMet, fMet) and undetermined tRNAs (Und-NNN) are automatically excluded as they serve specialized functions in translation initiation.
# Extract tRNA gene copy numbers for yeast
trna_gcn <- extract_trna_gcn(yeast_trna)
head(trna_gcn)
# View the distribution of tRNA gene copies
hist(trna_gcn, main = "Distribution of tRNA gene copy numbers")
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