MSstatsPTMSiteLocator: Locate modification site number and amino acid

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Locate modification site number and amino acid

Description

Locate modification site number and amino acid

Usage

MSstatsPTMSiteLocator(
  data,
  protein_name_col = "ProteinName",
  unmod_pep_col = "PeptideSequence",
  mod_pep_col = "PeptideModifiedSequence",
  clean_mod = FALSE,
  fasta_file = NULL,
  fasta_protein_name = "header",
  mod_id = "\\*",
  localization_scores = FALSE,
  localization_cutoff = 0.75,
  remove_unlocalized_peptides = TRUE,
  terminus_included = FALSE,
  terminus_id = "\\.",
  mod_id_is_numeric = FALSE,
  remove_underscores = FALSE,
  remove_other_mods = FALSE,
  bracket = FALSE,
  replace_text = FALSE
)

Arguments

data	data.table of enriched experimental run. Must include ProteinName, PeptideSequence, PeptideModifiedSequence, and (optionally) Start columns.
protein_name_col	Name of column indicating protein. Default is ProteinName.
unmod_pep_col	Name of column indicating unmodified peptide sequence. Default is PeptideSequence.
mod_pep_col	Name of column indicating modified peptide sequence. Default is PeptideModifiedSequence.
clean_mod	Remove special characters and numbers around modification name. Default is FALSE
fasta_file	File path to FASTA file that matches with proteins in data. Can be either string or data.table processed with tidyFasta() function. Default to NULL if peptide number included in data.
fasta_protein_name	Name of fasta file column that matches with protein_name_col. Default is header.
mod_id	String that indicates what amino acid was modified in PeptideSequence.
localization_scores	Boolean indicating if mod id is a localization score. If TRUE, mod_id will be ignored and localization cutoff will be used to determine sites. Default is FALSE.
localization_cutoff	Default is .75. Localization probabilities below cutoffs will be removed. localization_scores must be TRUE.
remove_unlocalized_peptides	Default is TRUE. If localization_scores is TRUE and probabilities are below localization_cutoff, the modification site will not be able to be determined. These unlocalized peptides can be kept or removed. If FALSE the unlocalized peptides will still be used in modeling the sites that could be localized.
terminus_included	Boolean indicating if the PeptideSequence includes the terminus amino acid.
terminus_id	String that indicates what the terminus amino acid is. Default is '.'.
mod_id_is_numeric	Boolean indicating if modification identifier is a number instead of a character (i.e. +80 vs *).
remove_underscores	Boolean indicating if underscores around peptide exist. These should be removed to properly count where in sequence the modification occurred.
remove_other_mods	keeping mods that are not of interest can mess up the amino acid count. Remove them if they are causing issues.
bracket	bracket type that encompasses PTM (usually [ or (). Always pass opening bracket (there is a function to grab the close bracket). Default is FALSE (i.e. no bracket).
replace_text	If PTM is noted by text (i.e. Phospho) and needs to be replaced by an indicator (*)

Value

data.table with site location added into Protein column.

Examples

##TODO

Vitek-Lab/MSstatsPTM documentation built on April 21, 2024, 6:45 a.m.