View source: R/translate_cds_to_protein.R
translate_cds_to_protein | R Documentation |
A helper function that takes a fasta
file storing coding sequences
as input and translates these coding sequences into amino acid sequences
storing them as fasta
output file.
translate_cds_to_protein(input_file, output_file, delete_corrupt_cds = FALSE)
input_file |
file path to |
output_file |
name or file path in which translated amino acid sequences (AA)
shall be stored as |
delete_corrupt_cds |
delete_corrupt_cds a logical value indicating whether sequences with corrupt base triplets should be removed from the input |
Hajk-Georg Drost
## Not run:
# install.packages("biomartr")
# download coding sequences of Arabidopsis thaliana
Ath_file_path <- biomartr::getCDS(db = "refseq",
organism = "Arabidopsis thaliana",
gunzip = TRUE)
# translate coding sequences into amino acid sequences
translate_cds_to_protein(Ath_file_path, "Ath_aa_seqs.fasta")
## End(Not run)
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