PTMlocate
annotates modified sites with associated peptides.
locatePTM(peptide, uniprot, fasta, modResidue, modSymbol, rmConfound = FALSE)
peptide | A string vector of peptide sequences. The peptide sequence does not include its preceding and following AAs. |
---|---|
uniprot | A string vector of Uniprot identifiers of the peptides' originating proteins. UniProtKB entry isoform sequence is used. |
fasta | A data.table with FASTA information. Output of |
modResidue | A string. Modifiable amino acid residues. |
modSymbol | A string. Symbol of a modified site. |
rmConfound | A logical. |
A data frame with three columns: uniprot_iso
, peptide
,
site
.
fasta <- tidyFasta("https://www.uniprot.org/uniprot/O13297.fasta") locatePTM("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")#> Warning: Both 'col_seq' and '..col_seq' exist in calling scope. Please remove the '..col_seq' variable in calling scope for clarity.#> Warning: Both 'col_fasta' and '..col_fasta' exist in calling scope. Please remove the '..col_fasta' variable in calling scope for clarity.#> Warning: Both 'col_res' and '..col_res' exist in calling scope. Please remove the '..col_res' variable in calling scope for clarity.#> uniprot_iso peptide site #> 1: O13297 DRVSYIHNDSC*TR C467