create_peptidome: Peptidome Generator

In rr-2/PeptideRanger:

Peptidome Generator

Description

Generates a tryptic peptidome of unique peptides using a provided proteome. Requires bioconductor pacakge "cleaver".

Usage

create_peptidome(proteome_dir, missed_cleavages, synth_peps, aa_range)

Arguments

proteome_dir	directory to proteome fasta file
missed_cleavages	range of missed cleavage events considered during in-silico digestion
synth_peps	If TRUE, filters out peptides that are problematic for peptide synthesis. Currnetly includes peptides with: N-term Q/E residues and C-term P residues
aa_range	range of peptide size by amino acid count included

Value

Peptidome of unique peptides with parent protein uniprot IDs, sequence locations in parent proteins, and n missed cleavages

Examples

## Not run: 
create_peptidome(proteome_dir = "./proteome.fasta",
                 missed_cleavages = c(0,2),
                 synth_peps = FALSE,
                 aa_range = c(7-25))

## End(Not run)

rr-2/PeptideRanger documentation built on May 27, 2023, 4:43 p.m.