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Add a column describing the position of the peptide sequence with respect to the protein

add_peptide_positions.Rd

Identify the position of the peptide sequence in the protein.

The peptide position is undefined (NA) if:

  1. The peptide sequence has multiple master proteins

  2. The protein does not exist in the proteome fasta

  3. The peptide is repeated in the protein sequence.

The peptide_position_info column details why the peptide positions columns are NA

Usage

add_peptide_positions(
  obj,
  proteome_fasta,
  master_protein_col = "Master.Protein.Accessions",
  protein_col_split = "; ",
  sequence_col = "Sequence"
)

Arguments

obj

SummarizedExperiment with PD output at PSM/peptide level

proteome_fasta

character Filepath for proteome fasta

master_protein_col

character Column name for master protein

protein_col_split

character Delimiter for multiple proteins in master_protein_col

sequence_col

character Column name for peptide sequence

Value

SummarizedExperiment with extra row columns detailing the peptide position