SkylinetoMSstatsFormat: Import Skyline files

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Import Skyline files

Description

Import Skyline files

Usage

SkylinetoMSstatsFormat(
  input,
  annotation = NULL,
  removeiRT = TRUE,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Feature = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	name of MSstats input report from Skyline, which includes feature-level data.
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.
removeiRT	TRUE (default) will remove the proteins or peptides which are labeled '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.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	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.
...	additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

skyline_raw = system.file("tinytest/raw_data/Skyline/skyline_input.csv",
                          package = "MSstatsConvert")
skyline_raw = data.table::fread(skyline_raw)
skyline_imported = SkylinetoMSstatsFormat(skyline_raw)
head(skyline_imported)

Vitek-Lab/MSstats documentation built on April 21, 2024, 10:14 p.m.