SkylinetoMSstatsPTMFormat: Convert Skyline output into MSstatsPTM format

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

Convert Skyline output into MSstatsPTM format

Description

Currently only supports label-free quantification.

Usage

SkylinetoMSstatsPTMFormat(
  input,
  fasta_path,
  fasta_protein_name = "uniprot_iso",
  annotation = NULL,
  input_protein = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  removeiRT = TRUE,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  use_unique_peptide = TRUE,
  remove_few_measurements = FALSE,
  remove_oxidation_peptides = FALSE,
  removeProtein_with1Feature = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input	name of Skyline PTM output
fasta_path	A string of path to a FASTA file, used to match PTM peptides.
fasta_protein_name	Name of fasta column that matches with protein name in evidence file. Default is uniprot_iso.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
input_protein	name of Skyline unmodified protein output (optional)
annotation_protein	name of 'annotation.txt' data which includes Condition, BioReplicate, Run for unmodified protein output. This can be the same as annotation.
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.
removeiRT	TRUE (default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for DetectionQValue. default is 0.01.
use_unique_peptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
remove_few_measurements	TRUE will remove the features that have 1 or 2 measurements across runs. FALSE is default.
remove_oxidation_peptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
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.