Extract modification counts from one or more peptide sequences

Given a character vector of peptide sequences containing modifications in any annotation style (deltaMass, UniMod ID, or name), returns a named integer vector with the count of each unique modification. Regardless of the input annotation style, all modifications are converted to their UniMod name in the output (e.g. `[+79.966]` and `[UNIMOD:21]` both appear as `Phospho`).

getModificationsCounts(sequences)

Arguments

sequences

A `character()` vector of peptide sequences in ProForma format.

Value

A named integer vector where names are UniMod modification names and values are their occurrence counts across all input sequences. Returns an empty integer vector if no modifications are found.

Author

Guillaume Deflandre <guillaume.deflandre@uclouvain.be>

Examples

seqs <- c(
    "[+304]-AT[Phospho]K",
    "AC[Carbamidomethyl]T[+79.966]S[Phospho]K",
    "PEPTIDE"
)
getModificationsCounts(seqs)
#>            +304 Carbamidomethyl         Phospho 
#>               1               1               3