PStoMSstatsPTMFormat: Convert Peaks Studio output into MSstatsPTM format

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

Convert Peaks Studio output into MSstatsPTM format

Description

Currently only supports label-free quantification.

Usage

PStoMSstatsPTMFormat(
  input,
  annotation,
  input_protein = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  target_modification = NULL,
  remove_oxidation_peptides = FALSE,
  remove_multi_mod_types = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input	name of Peaks Studio PTM output
annotation	name of annotation file which includes Raw.file, Condition, BioReplicate, Run. For example annotation see example below.
input_protein	name of Peaks Studio unmodified protein output (optional)
annotation_protein	name of annotation file which includes Raw.file, Condition, BioReplicate, Run for unmodified protein output.
use_unmod_peptides	Boolean if the unmodified peptides in the input file should be used to construct the unmodified protein output. Only used if input_protein is not provided. Default is FALSE
target_modification	Character name of modification of interest. To use all mod types, leave as NULL. Default is NULL. Note that if the name includes special characters, you must include "\" before the characters. Ex. "Phosphorylation \(STY\)"
remove_oxidation_peptides	Boolean if Oxidation (M) modifications should be removed. Default is FALSE
remove_multi_mod_types	Used if target_modification is not NULL. TRUE will remove peptides with multiple types of modifications (ie acetylation and phosphorylation). FALSE will keep these peptides and summarize them seperately.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing wil be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.

Value

list of data.table

Examples

# The output should be in the following format.
head(raw.input$PTM)
head(raw.input$PROTEIN)

Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.m.