Files in MSstatsConvert

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

NEWS.md README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

R/utils_dt_operations.R R/utils_shared_peptides.R R/clean_Progenesis.R R/utils_classes.R R/clean_MaxQuant.R R/clean_ProteomeDiscoverer.R R/utils_fractions.R R/clean_OpenSWATH.R R/clean_Spectronaut.R R/utils_clean_features.R R/MSstatsConvert_core_functions.R R/clean_DIAUmpire.R R/clean_OpenMS.R R/utils_balanced_design.R R/utils_MSstatsConvert.R R/utils_logging.R R/utils_filtering.R R/clean_SpectroMine.R R/utils_checks.R R/utils_annotation.R R/clean_Skyline.R vignettes/msstats_data_format.Rmd man/dot-handleFractionsTMT.Rd man/MSstatsInputFiles.Rd man/dot-standardizeColnames.Rd man/dot-checkAnnotation.Rd man/dot-cleanRawOpenSWATH.Rd man/dot-checkDDA.Rd man/getInputFile.Rd man/dot-handleFiltering.Rd man/dot-cleanRawMaxQuant.Rd man/MSstatsConvert.Rd man/dot-filterOverlapped.Rd man/dot-checkDuplicatedMeasurements.Rd man/dot-logSuccess.Rd man/dot-filterFewMeasurements.Rd man/dot-checkOverlappedFeatures.Rd man/dot-filterByPattern.Rd man/dot-cleanRawSkyline.Rd man/dot-cleanRawPDMSstats.Rd man/dot-getChannelColumns.Rd man/dot-nullAppender.Rd man/dot-summarizeMultiplePSMs.Rd man/dot-mergeAnnotation.Rd man/dot-getOverlappingFeatures.Rd man/dot-cleanRawPDTMT.Rd man/dot-summarizeMultipleMeasurements.Rd man/MSstatsPreprocess.Rd man/dot-cleanRawPD.Rd man/MSstatsImport.Rd man/dot-makeScoreFilterMessage.Rd man/dot-cleanRawSpectroMineTMT.Rd man/dot-cleanRawSpectronaut.Rd man/MSstatsSaveSessionInfo.Rd man/dot-fillValues.Rd man/dot-makeExactFilterMessage.Rd man/dot-cleanRawDIAUmpire.Rd man/dot-fixColumnTypes.Rd man/dot-removeSharedPeptides.Rd man/dot-filterManyColumns.Rd man/dot-cleanByFeature.Rd man/dot-selectMSstatsColumns.Rd man/dot-getDataTable.Rd man/dot-removeOverlappingFeatures.Rd man/MSstatsBalancedDesign.Rd man/dot-findAvailable.Rd man/dot-fixMissingValues.Rd man/dot-cleanRawProgenesis.Rd man/getDataType.Rd man/dot-cleanRawOpenMS.Rd man/dot-handleIsotopicPeaks.Rd man/dot-checkMSstatsParams.Rd man/dot-onLoad.Rd man/dot-getMissingRunsPerFeature.Rd man/dot-aggregatePSMstoPeptideIons.Rd man/dot-handleSingleFeaturePerProtein.Rd man/dot-handleFractionsLF.Rd man/dot-MSstatsFormat.Rd man/dot-getCorrectFraction.Rd man/dot-makeBalancedDesign.Rd man/dot-adjustIntensities.Rd man/dot-countCommonFeatures.Rd man/dot-filterExact.Rd man/dot-filterByScore.Rd man/dot-handleFractions.Rd man/dot-getFullDesign.Rd man/dot-logConverterOptions.Rd man/MSstatsLogsSettings.Rd man/dot-handleSharedPeptides.Rd man/dot-addFractions.Rd man/MSstatsClean.Rd man/dot-checkMultiRun.Rd man/MSstatsMakeAnnotation.Rd tests/tinytest.R

inst/doc/msstats_data_format.html

inst/doc/msstats_data_format.R inst/doc/msstats_data_format.Rmd inst/tinytest/test_filtering.R inst/tinytest/test_workflow.R

inst/tinytest/get_dt_test.csv

inst/tinytest/test_dt.R inst/tinytest/test_annotation.R inst/tinytest/test_fractions.R inst/tinytest/test_shared_peptides.R inst/tinytest/test_logging.R inst/tinytest/test_MSstatsConvert.R inst/tinytest/test_cleanRaw.R inst/tinytest/test_feature_cleaning.R inst/tinytest/test_balanced_design.R

inst/tinytest/raw_data/unbalanced_data.csv

inst/tinytest/raw_data/Progenesis/progenesis_annot.csv

inst/tinytest/raw_data/Progenesis/progenesis_input.csv

inst/tinytest/raw_data/MaxQuant/mq_pg.csv

inst/tinytest/raw_data/MaxQuant/mq_ev.csv

inst/tinytest/raw_data/MaxQuant/annotation.csv

inst/tinytest/raw_data/OpenSWATH/openswath_input.csv

inst/tinytest/raw_data/DIAUmpire/dia_frag.csv

inst/tinytest/raw_data/DIAUmpire/dia_pept.csv

inst/tinytest/raw_data/DIAUmpire/dia_prot.csv

inst/tinytest/raw_data/OpenMS/openms_input.csv

inst/tinytest/raw_data/MaxQuantTMT/mq_pg.csv

inst/tinytest/raw_data/MaxQuantTMT/mq_ev.csv

inst/tinytest/raw_data/PDTMT/pdtmt_input.csv

inst/tinytest/raw_data/PD/pd_input.csv

inst/tinytest/raw_data/Spectronaut/spectronaut_input.csv

inst/tinytest/raw_data/SpectroMine/spectromine_input.csv

inst/tinytest/raw_data/Skyline/skyline_input.csv

inst/tinytest/raw_data/OpenMSTMT/openmstmt_input.csv

MSstatsConvert documentation built on Nov. 8, 2020, 5:49 p.m.