OpenSWATHtoMSstatsFormat: Import OpenSWATH files

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

Import OpenSWATH files

Description

Import OpenSWATH files

Usage

OpenSWATHtoMSstatsFormat(
  input,
  annotation,
  filter_with_mscore = TRUE,
  mscore_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	name of MSstats input report from OpenSWATH, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename.
filter_with_mscore	TRUE(default) will filter out the features that have greater than mscore_cutoff in m_score column. Those features will be removed.
mscore_cutoff	Cutoff for m_score. 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.
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.
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.
...	additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek.

Examples

os_raw = system.file("tinytest/raw_data/OpenSWATH/openswath_input.csv", 
                             package = "MSstatsConvert")
annot = system.file("tinytest/annotations/annot_os.csv", 
                    package = "MSstats")
os_raw = data.table::fread(os_raw) 
annot = data.table::fread(annot)

os_imported = OpenSWATHtoMSstatsFormat(os_raw, annot, use_log_file = FALSE)
head(os_imported)

MeenaChoi/MSstats documentation built on Nov. 30, 2024, 7:26 a.m.