SkylinetoMSstatsFormat: Import Skyline files

View source: R/converters.R

SkylinetoMSstatsFormatR Documentation

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)


MeenaChoi/MSstats documentation built on July 13, 2024, 10:59 a.m.