Add peptide positions with respect to the protein

This function takes a SummarizedExperiment object and adds rowData columns to describe the positions of the peptides within the proteins', taking into account the possible peptides according to the digestion enzyme used.

Usage

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

Arguments

obj

SummarizedExperiment. Proteomics dataset

proteome_fasta

character filepath to fasta with protein sequences

digest_enzyme

character. Enzyme used. See ?cleaver::cleave

missed_cleavages

numeric. Vector of allowed number of missed cleavages

master_protein_col

character. Name of column containing master proteins

sequence_col

character. Name of column containing peptide sequences

start_col

character. Name of output column containing peptide start positions

end_col

character. Name of output column containing peptide end positions

Value

Returns a SummarizedExperiment with additional rowData columns describing peptide start and end positions with respect to the protein