Man pages for Vitek-Lab/MSstatsConvert
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
| as.data.frame.MSstatsValidated | Convert output of converters to data.frame |
| as.data.table.MSstatsValidated | Convert output of converters to data.table |
| DIANNtoMSstatsFormat | Import Diann files |
| DIAUmpiretoMSstatsFormat | Import DIA-Umpire files |
| dot-addFractions | Add a Fraction column to the output of 'MSstatsPreprocess' |
| dot-adjustIntensities | Fix invalid intensities: infinite to NA, between 0 and 1 to 0 |
| dot-aggregatePSMstoPeptideIons | Aggregate multiple PSMs to a single peptide ion. |
| dot-checkAnnotation | Check if the annotation is valid |
| dot-checkDDA | Check validity of DDA data |
| dot-checkDuplicatedMeasurements | Check if there are duplicated measurements within run |
| dot-checkMSstatsParams | Check validity of parameters to the 'MSstatsImport' function. |
| dot-checkMultiRun | Check if fractionation exists |
| dot-checkOverlappedFeatures | Check if any features are measured in multiple fractions |
| dot-cleanByFeature | Perform by-feature operations. |
| dot-cleanRawDIANN | Clean raw Diann files |
| dot-cleanRawDIAUmpire | Clean raw DIAUmpire files |
| dot-cleanRawMaxQuant | Clean raw output from MaxQuant |
| dot-cleanRawMetamorpheus | Clean raw Metamorpheus files |
| dot-cleanRawOpenMS | Clean raw output from OpenMS |
| dot-cleanRawOpenSWATH | Clean raw OpenSWATH files |
| dot-cleanRawPD | Clean raw Proteome Discoverer data |
| dot-cleanRawPDMSstats | Clean raw PD output |
| dot-cleanRawPDTMT | Clean raw TMT data from Proteome Discoverer |
| dot-cleanRawPhilosopher | Clean raw Philosopher files |
| dot-cleanRawProgenesis | Clean raw Progenesis output |
| dot-cleanRawSkyline | Clean raw data from Skyline |
| dot-cleanRawSpectroMineTMT | Clean raw SpectroMine TMT data |
| dot-cleanRawSpectronaut | Clean raw Spectronaut output. |
| dot-countCommonFeatures | Get common values from two vectors of features |
| dot-fillValues | Set column to a single value |
| dot-filterByPattern | Handle filtering by pattern |
| dot-filterByScore | Filter PSMs / proteins by a given score column. |
| dot-filterExact | Filter out specified symbols. |
| dot-filterFewMeasurements | Remove features with a small number of (non-missing)... |
| dot-filterManyColumns | Filter rows that contain specifed symbols in multiple... |
| dot-filterOverlapped | Remove overlapped features |
| dot-findAvailable | Select an available options from a set of possibilities |
| dot-fixBasicColumns | Remove underscores from sequences and change intensity type... |
| dot-fixColumnTypes | Change classes of multiple columns |
| dot-fixMissingValues | Change labels for missing values |
| dot-getChannelColumns | Get intensity columns from wide-format data |
| dot-getCorrectFraction | Get a name of fraction with the largest number of... |
| dot-getDataTable | Read file from a provided path or convert given data.frame to... |
| dot-getFullDesign | Create a data.frame of each combination of values for given... |
| dot-getMissingRunsPerFeature | Get names of missing runs |
| dot-getOverlappingFeatures | Get features that are overlapped among multiple runs |
| dot-handleFiltering | Handle PSM/proteins scores |
| dot-handleFractions | Check if there are overlapping features and remove if needed |
| dot-handleFractionsLF | Handle overlapping features |
| dot-handleFractionsTMT | Remove peptide ions overlapped among multiple fractions of... |
| dot-handleIsotopicPeaks | Handle isotopic peaks |
| dot-handleSharedPeptides | Handle shared peptides. |
| dot-handleSingleFeaturePerProtein | Remove proteins only identified by a single feature |
| dot-logConverterOptions | Log information about converter options |
| dot-logSuccess | Make a message about successful data cleaning/importing |
| dot-makeBalancedDesign | Fill missing rows to create balanced design |
| dot-makeExactFilterMessage | Make a message about filtering based on fixed values |
| dot-makeScoreFilterMessage | Make a message about filtering based on a score |
| dot-mergeAnnotation | Merge annotation with feature data |
| dot-MSstatsFormat | Output format for further analysis by MSstats |
| dot-nullAppender | log4r appender used not to write messages |
| dot-onLoad | Set default logging object when package is loaded |
| dot-removeOverlappingFeatures | Replace intensities of overlapped fractions with NA, keeping... |
| dot-removeSharedPeptides | Remove peptides assigned to more than one protein. |
| dot-selectMSstatsColumns | Select columns for MSstats format |
| dot-sharedParametersAmongConverters | A dummy function to store shared documentation items for... |
| dot-standardizeColnames | Change column names to match read.table/read.csv/read.delim... |
| dot-summarizeMultipleMeasurements | Summarize multiple measurements per feature in a single run |
| dot-summarizeMultiplePSMs | Pick one PSM from a data.table of several PSMs. |
| dot-validatePDTMTInputColumns | Helper method to validate input has necessary columns |
| FragPipetoMSstatsFormat | Import FragPipe files |
| getDataType | Get type of dataset from an MSstatsInputFiles object. |
| getInputFile | Get one of files contained in an instance of... |
| MaxQtoMSstatsFormat | Import MaxQuant files |
| MetamorpheusToMSstatsFormat | Import Metamorpheus files |
| MSstatsBalancedDesign | Creates balanced design by removing overlapping fractions and... |
| MSstatsClean | Clean files generated by a signal processing tools. |
| MSstatsConvert | MSstatsConvert: An R Package to Convert Data from Mass... |
| MSstatsImport | Import files from signal processing tools. |
| MSstatsInputFiles | Class to model files that describe a single MS dataset. |
| MSstatsLogsSettings | Set how MSstats will log information from data processing |
| MSstatsMakeAnnotation | Create annotation |
| MSstatsPreprocess | Preprocess outputs from MS signal processing tools for... |
| MSstatsSaveSessionInfo | Save session information |
| OpenMStoMSstatsFormat | Import OpenMS files |
| OpenSWATHtoMSstatsFormat | Import OpenSWATH files |
| PDtoMSstatsFormat | Import Proteome Discoverer files |
| ProgenesistoMSstatsFormat | Import Progenesis files |
| ProteinProspectortoMSstatsTMTFormat | Generate MSstatsTMT required input format from Protein... |
| SkylinetoMSstatsFormat | Import Skyline files |
| SpectronauttoMSstatsFormat | Import Spectronaut files |
