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