OpenSWATHtoMSstatsFormat {MSstats} | R Documentation |
Import OpenSWATH files
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, ... )
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'. |
data.frame in the MSstats required format.
Meena Choi, Olga Vitek.
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)