SkylinetoMSstatsFormat.RdImport 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.
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)#> INFO [2021-07-05 20:05:32] ** Raw data from Skyline imported successfully. #> INFO [2021-07-05 20:05:32] ** Raw data from Skyline cleaned successfully. #> INFO [2021-07-05 20:05:32] ** Using annotation extracted from quantification data. #> INFO [2021-07-05 20:05:32] ** Run labels were standardized to remove symbols such as '.' or '%'. #> INFO [2021-07-05 20:05:32] ** The following options are used: #> - Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge #> - Shared peptides will be removed. #> - Proteins with single feature will not be removed. #> - Features with less than 3 measurements across runs will be removed. #> INFO [2021-07-05 20:05:32] ** Rows with values of StandardType equal to iRT are removed #> INFO [2021-07-05 20:05:32] ** Intensities with values of Truncated equal to TRUE are replaced with NA #> WARN [2021-07-05 20:05:32] ** DetectionQValue not found in input columns. #> INFO [2021-07-05 20:05:32] ** Sequences containing DECOY, Decoys are removed. #> INFO [2021-07-05 20:05:32] ** Three isotopic preaks per feature and run are summed #> INFO [2021-07-05 20:05:32] ** Features with all missing measurements across runs are removed. #> INFO [2021-07-05 20:05:32] ** Shared peptides are removed. #> INFO [2021-07-05 20:05:32] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum #> INFO [2021-07-05 20:05:32] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:32] ** Run annotation merged with quantification data. #> INFO [2021-07-05 20:05:32] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:32] ** Fractionation handled. #> INFO [2021-07-05 20:05:32] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-07-05 20:05:32] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.head(skyline_imported)#> ProteinName PeptideSequence PrecursorCharge FragmentIon ProductCharge #> 1 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> 2 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> 3 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> 4 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> 5 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> 6 P00370 AANAGGVATSGLEMAQNAAR 3 NA NA #> IsotopeLabelType Condition BioReplicate #> 1 light Mix1 1 #> 2 light Mix1 2 #> 3 light Mix1 3 #> 4 light Mix2 4 #> 5 light Mix2 5 #> 6 light Mix2 6 #> Run Fraction Intensity #> 1 121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1raw 1 5311459776 #> 2 121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2raw 1 4900185344 #> 3 121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3raw 1 5323685504 #> 4 121219_S_CCES_01_04_LysC_Try_1to10_Mixt_2_1raw 1 5327922240 #> 5 121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2raw 1 5824830336 #> 6 121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3raw 1 5674675584