Purpose of MSstatsConvert | MSstats data format | Logging | Importing and cleaning data | Preprocessing | Fractions and balanced design | Metabolomics with MZMine | Annotation levels and the SIRIUS option
Package: MSstatsConvert 1.23.2
Anthony Wu
MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.
Authors:
MSstatsConvert_1.23.2.tar.gz
MSstatsConvert_1.23.2.zip(r-4.7)MSstatsConvert_1.23.2.zip(r-4.6)MSstatsConvert_1.23.2.zip(r-4.5)
MSstatsConvert_1.23.2.tgz(r-4.6-x86_64)MSstatsConvert_1.23.2.tgz(r-4.6-arm64)MSstatsConvert_1.23.2.tgz(r-4.5-x86_64)MSstatsConvert_1.23.2.tgz(r-4.5-arm64)
MSstatsConvert_1.23.2.tar.gz(r-4.7-arm64)MSstatsConvert_1.23.2.tar.gz(r-4.7-x86_64)MSstatsConvert_1.23.2.tar.gz(r-4.6-arm64)MSstatsConvert_1.23.2.tar.gz(r-4.6-x86_64)
MSstatsConvert_1.23.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MSstatsConvert/json (API)
| # Install 'MSstatsConvert' in R: |
| install.packages('MSstatsConvert', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:MSstatsConvert-1.23.2(bioc 3.24)MSstatsConvert-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
massspectrometryproteomicssoftwaredataimportqualitycontrolcpp
Last updated from:dbf8afb0ad. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 147 | ||
| linux-devel-arm64 | NOTE | 199 | ||
| linux-devel-x86_64 | NOTE | 196 | ||
| source / vignettes | OK | 217 | ||
| linux-release-arm64 | NOTE | 178 | ||
| linux-release-x86_64 | NOTE | 173 | ||
| macos-release-arm64 | NOTE | 140 | ||
| macos-release-x86_64 | NOTE | 394 | ||
| macos-oldrel-arm64 | NOTE | 141 | ||
| macos-oldrel-x86_64 | NOTE | 296 | ||
| windows-devel | NOTE | 175 | ||
| windows-release | NOTE | 124 | ||
| windows-oldrel | NOTE | 128 | ||
| wasm-release | OK | 114 |
Exports:CheckDataHealthDIANNtoMSstatsFormatDIAUmpiretoMSstatsFormatFragPipetoMSstatsFormatgetDataTypegetInputFileMaxQtoMSstatsFormatMaxQtoMSstatsTMTFormatMetamorpheusToMSstatsFormatMSstatsAnomalyScoresMSstatsBalancedDesignMSstatsCleanMSstatsImportMSstatsLogsSettingsMSstatsMakeAnnotationMSstatsPreprocessMSstatsSaveSessionInfoMZMinetoMSstatsFormatOpenMStoMSstatsFormatOpenMStoMSstatsTMTFormatOpenSWATHtoMSstatsFormatPDtoMSstatsFormatPDtoMSstatsTMTFormatPhilosophertoMSstatsTMTFormatProgenesistoMSstatsFormatProteinProspectortoMSstatsTMTFormatSkylinetoMSstatsFormatSpectroMinetoMSstatsTMTFormatSpectronauttoMSstatsFormat
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clean raw Proteome Discoverer data | .cleanRawPD |
| Convert output of converters to data.frame | as.data.frame.MSstatsValidated |
| Convert output of converters to data.table | as.data.table.MSstatsValidated |
| Takes as input the output of the SpectronauttoMSstatsFormat function and calculates various quality metrics to assess the health of the data. Requires Anomaly Detection model to be fit. | CheckDataHealth |
| Import Diann files | DIANNtoMSstatsFormat |
| Import DIA-Umpire files | DIAUmpiretoMSstatsFormat |
| Import FragPipe files | FragPipetoMSstatsFormat |
| Get one of files contained in an instance of 'MSstatsInputFiles' class. | getInputFile getInputFile,MSstatsInputFiles-method getInputFile,MSstatsPhilosopherFiles-method |
| Import MaxQuant files | MaxQtoMSstatsFormat |
| Generate MSstatsTMT required input format from MaxQuant output | MaxQtoMSstatsTMTFormat |
| Import Metamorpheus files | MetamorpheusToMSstatsFormat |
| Run Anomaly Model | MSstatsAnomalyScores |
| Creates balanced design by removing overlapping fractions and filling incomplete rows | MSstatsBalancedDesign |
| Clean files generated by a signal processing tools. | MSstatsClean MSstatsClean,MSstatsDIANNFiles-method MSstatsClean,MSstatsDIAUmpireFiles-method MSstatsClean,MSstatsMaxQuantFiles-method MSstatsClean,MSstatsMetamorpheusFiles-method MSstatsClean,MSstatsMZMineFiles-method MSstatsClean,MSstatsOpenMSFiles-method MSstatsClean,MSstatsOpenSWATHFiles-method MSstatsClean,MSstatsPhilosopherFiles-method MSstatsClean,MSstatsProgenesisFiles-method MSstatsClean,MSstatsProteinProspectorFiles-method MSstatsClean,MSstatsProteomeDiscovererFiles-method MSstatsClean,MSstatsSkylineFiles-method MSstatsClean,MSstatsSpectroMineFiles-method MSstatsClean,MSstatsSpectronautFiles-method |
| Import files from signal processing tools. | MSstatsImport |
| Set how MSstats will log information from data processing | MSstatsLogsSettings |
| Create annotation | MSstatsMakeAnnotation |
| Preprocess outputs from MS signal processing tools for analysis with MSstats | MSstatsPreprocess |
| Save session information | MSstatsSaveSessionInfo |
| Import MZMine files | MZMinetoMSstatsFormat |
| Import OpenMS files | OpenMStoMSstatsFormat |
| Generate MSstatsTMT required input format for OpenMS output | OpenMStoMSstatsTMTFormat |
| Import OpenSWATH files | OpenSWATHtoMSstatsFormat |
| Import Proteome Discoverer files | PDtoMSstatsFormat |
| Convert Proteome Discoverer output to MSstatsTMT format. | PDtoMSstatsTMTFormat |
| Convert Philosopher (Fragpipe) output to MSstatsTMT format. | PhilosophertoMSstatsTMTFormat |
| Import Progenesis files | ProgenesistoMSstatsFormat |
| Generate MSstatsTMT required input format from Protein Prospector output | ProteinProspectortoMSstatsTMTFormat |
| Import Skyline files | SkylinetoMSstatsFormat |
| Import data from SpectroMine | SpectroMinetoMSstatsTMTFormat |
| Import Spectronaut files | SpectronauttoMSstatsFormat |
