OpenMStoMSstatsFormat.RdImport OpenMS files
OpenMStoMSstatsFormat( input, annotation = NULL, 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 OpenMS, which includes feature(peptide ion)-level data. |
|---|---|
| annotation | name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename. |
| 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.
openms_raw = data.table::fread(system.file("tinytest/raw_data/OpenMS/openms_input.csv", package = "MSstatsConvert")) openms_imported = OpenMStoMSstatsFormat(openms_raw, use_log_file = FALSE)#> INFO [2021-07-05 20:05:31] ** Raw data from OpenMS imported successfully. #> INFO [2021-07-05 20:05:31] ** Raw data from OpenMS cleaned successfully. #> INFO [2021-07-05 20:05:31] ** Using annotation extracted from quantification data. #> INFO [2021-07-05 20:05:31] ** Run labels were standardized to remove symbols such as '.' or '%'. #> INFO [2021-07-05 20:05:31] ** The following options are used: #> - Features will be defined by the columns: 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 20:05:31] ** Features with all missing measurements across runs are removed. #> INFO [2021-07-05 20:05:31] ** Shared peptides are removed. #> INFO [2021-07-05 20:05:31] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max #> INFO [2021-07-05 20:05:31] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:31] ** Run annotation merged with quantification data. #> INFO [2021-07-05 20:05:31] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:31] ** Fractionation handled. #> INFO [2021-07-05 20:05:31] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-07-05 20:05:31] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.head(openms_imported)#> ProteinName PeptideSequence PrecursorCharge FragmentIon #> 1 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> 2 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> 3 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> 4 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> 5 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> 6 sp|P32602|SEC17_YEAST ALDGQYIEASDIYSK 2 NA #> ProductCharge IsotopeLabelType Condition BioReplicate Run Fraction Intensity #> 1 0 L 1 1 1 1 57341200 #> 2 0 L 4 4 10 1 71823800 #> 3 0 L 4 4 11 1 65957500 #> 4 0 L 4 4 12 1 56110700 #> 5 0 L 1 1 2 1 77898600 #> 6 0 L 1 1 3 1 49719500