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