Evaluate peptide termini against theoretical cleavage positions — add_tryptic_termini_flags • biomasslmb

Evaluate peptide termini against theoretical cleavage positions

Usage

add_tryptic_termini_flags(
  obj,
  proteome_fasta,
  digest_enzyme = "trypsin-simple",
  missed_cleavages = c(0, 1, 2),
  master_protein_col = "Leading.razor.protein",
  start_col = "start",
  end_col = "end"
)

Arguments

obj: SummarizedExperiment
proteome_fasta: character. Path to FASTA file
digest_enzyme: character. Enzyme for cleaver::cleavageRanges
missed_cleavages: numeric vector. Allowed missed cleavages
master_protein_col: character. Column in rowData containing protein IDs
start_col: character. Column containing peptide start positions
end_col: character. Column containing peptide end positions

Value

SummarizedExperiment with additional rowData columns: N_tryp and C_tryp