Man pages for MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

checkRepeatedDesignCheck if data represents repeated measurements design
dataProcessProcess MS data: clean, normalize and summarize before...
dataProcessPlotsVisualization for explanatory data analysis
DDARawDataExample dataset from a label-free DDA, a controlled spike-in...
DDARawData.SkylineExample dataset from a label-free DDA, a controlled spike-in...
designSampleSizePlanning future experimental designs of Selected Reaction...
designSampleSizePlotsVisualization for sample size calculation
DIANNtoMSstatsFormatImport Diann files
DIARawDataExample dataset from a label-free DIA, a group comparison...
DIAUmpiretoMSstatsFormatImport DIA-Umpire files
dot-addCoverageInfoAdd coverage information to a data.table
dot-addModelInformationAdd model information
dot-addModelVariancesAdd model variances
dot-addNInformativeInfoAdd information about number of informative features
dot-addNoisyFlagAdd flag for noisy features
dot-addOutlierCutoffAdd outlier cutoff
dot-addOutlierInformationAdd flag for outlier
dot-addSurvivalPredictionsGet predicted values from a survival model
dot-adjustLRunsAdjust summarized abundance based on the heavy channel
dot-calculateOutlierCutoffCalculate cutoff to label outliers
dot-calculatePowerPower calculation
dot-calculateProteinVarianceCalculate protein variances
dot-checkContrastMatrixCheck if contrast matrix includes all conditions
dot-checkDataProcessParamsCheck validity of parameters to dataProcess function
dot-checkExperimentDesignCheck if a given column exists in the data
dot-checkGCPlotsInputCheck groupComparisonPlots parameters
dot-checkGroupComparisonInputCheck if groupComparison input was processed by the...
dot-checkSingleFeatureCheck if data has less than two features
dot-checkSingleLabelProteinsCheck if there are proteins with a single label in a labeled...
dot-checkSingleSubjectCheck if there is only single subject
dot-checkTechReplicateCheck if there are technical replicates
dot-checkUnProcessedDataValidityCheck validity of data that were not processed by MSstats...
dot-countInformativeCount informative features
dot-countMissingPercentageCount percentage of missing values in given conditions
dot-documentFunctionA dummy function to store shared documentation items.
dot-finalizeInputAdd summary statistics to dataProcess output
dot-finalizeLinearSummary statistics for linear model-based summarization
dot-finalizeTMPSummary statistics for output of TMP-based summarization
dot-fitHuberWrapper to fit robust linear model for one protein
dot-fitLinearModelFit a linear model
dot-fitModelForGroupComparisonChoose a model type (fixed/mixed effects) and fit it for a...
dot-fitModelSingleProteinFit model and perform group comparison for a single protein
dot-fitTukeyFit tukey median polish for a data matrix
dot-flagLowCoverageFlag for low coverage features
dot-flagUninformativeSingleLabelFlag uninformative features
dot-getAllComparisonsGet all comparisons for a single protein and a contrast...
dot-getColorKeyGGPlot2Create colorkey for ggplot2 heatmap
dot-getColorKeyPlotlyCreate colorkey for plotly heatmap
dot-getContrastCreate a contrast for a model with only group as a fixed...
dot-getContrastLabelsGet labels for contrasts
dot-getEmptyComparisonComparison output when there are measurements only in a...
dot-getFeatureVariancesCalculate variances of features
dot-getMedianGet median of protein abundances for a given label
dot-getMedianSigmaSubjectGet median per subject or group by subject
dot-getMinUtility function: get 0.99 * minimum of non-missing values
dot-getModelParametersGet params (coefficients, covariance matrix, degrees of...
dot-getNonMissingFilterIdentify non-missing values
dot-getNonMissingFilterStatsGet a logical vector for non-missing values to calculate...
dot-getNumSampleGet sample size
dot-getSingleProteinForProfileGet data for a single protein to plot
dot-getVarComponentGet variances from models fitted by the groupComparison...
dot-getWideTableUtility function for quantile normalization - get table in...
dot-getYaxisGet name for y-axis
dot-groupComparisonWithMultipleCoresPerform group comparison per protein in parallel
dot-groupComparisonWithSingleCorePerform group comparison per protein iteratively with a...
dot-handleEmptyConditionsHandle contrast when some of the conditions are missing
dot-handleSingleContrastGroup comparison for a single contrast
dot-isSummarizableCheck if a protein can be summarized with TMP
dot-logDatasetInformationLog information about feature-level data
dot-logMissingnessLog information about missing data
dot-logSingleLabeledProteinsPrint proteins with a single label to the log file
dot-logSummaryStatisticsPrint summary statistics to the log file
dot-makeComparisonCreate comparison plot
dot-makeConditionPlotMake condition plot
dot-makeFactorColumnsMake factor columns where needed
dot-makeHeatmapPlotlyCreate heatmap
dot-makeProfilePlotCreate profile plot
dot-makeQCPlotMake QC plot
dot-makeSummaryProfilePlotMake summary profile plot
dot-makeVolcanoCreate a volcano plot
dot-nicePrintPrint a table nicely
dot-normalizeGlobalStandardsNormalization based on standards
dot-normalizeMedianMedian normalization
dot-normalizeQuantileQuantile normalization based on the 'preprocessCore' package
dot-onLoadSet default logging object when package is loaded
dot-plotComparisonPreprocess data for comparison plots and create them
dot-plotHeatmapPrepare data for heatmaps and plot them
dot-plotVolcanoPreprocess data for volcano plots and create them
dot-prepareForDataProcessCheck validity of data already processed by MSstats converter
dot-prepareLinearPrepare feature-level data for linear summarization
dot-prepareSingleProteinForGCPrepare data for a single protein for group comparison
dot-prepareSummaryPrepare feature-level data for summarization
dot-prepareTMPPrepare feature-level data for TMP summarization
dot-preProcessIntensitiesCreate ABUNDANCE column and log-transform intensities
dot-quantileNormalizationSingleLabelQuantile normalization for a single label
dot-replaceZerosWithNAUtility function for normalization: replace 0s by NA
dot-runTukeyFit Tukey median polish
dot-saveSessionInfoSave information about R session to sessionInfo.txt file.
dot-saveTableSave a data table to a file
dot-selectHighQualityFeaturesSelect features of high quality
dot-selectTopFeaturesSelect features with highest average abundance
dot-setCensoredByThresholdSet censored values based on minimum in run/feature/run or...
dot-updateColumnsForProcessingCreate columns for data processing
dot-updateUnequalVariancesAdjust model for unequal variances
extractSDRFExtract experimental design from MSstats format into SDRF...
FragPipetoMSstatsFormatImport FragPipe files
getProcessedGet feature-level data to be used in the...
getSamplesInfoGet information about number of measurements for each group
getSelectedProteinsGet proteins based on names or integer IDs
groupComparisonWhole plot testing
groupComparisonPlotsVisualization for model-based analysis and summarizing...
makePeptidesDictionaryPrepare a peptides dictionary for global standards...
MaxQtoMSstatsFormatImport MaxQuant files
modelBasedQCPlotsVisualization for model-based quality control in fitting...
MSstatsContrastMatrixCreate a contrast matrix for groupComparison function
MSstatsGroupComparisonGroup comparison
MSstatsGroupComparisonOutputCreate output of group comparison based on results for...
MSstatsGroupComparisonSingleProteinGroup comparison for a single protein
MSstatsHandleMissingHandle censored missing values
MSstatsMergeFractionsRe-format the data before feature selection
MSstatsNormalizeNormalize MS data
MSstatsPrepareForDataProcessPrepare data for processing by 'dataProcess' function
MSstatsPrepareForGroupComparisonPrepare output for dataProcess for group comparison
MSstatsPrepareForSummarizationPrepare feature-level data for protein-level summarization
MSstatsSelectFeaturesFeature selection before feature-level data summarization
MSstatsSummarizationOutputPost-processing output from MSstats summarization
MSstatsSummarizeFeature-level data summarization
MSstatsSummarizeSingleLinearLinear model-based summarization for a single protein
MSstatsSummarizeSingleTMPTukey Median Polish summarization for a single protein
MSstatsSummarizeWithMultipleCoresFeature-level data summarization with multiple cores
OpenMStoMSstatsFormatImport OpenMS files
OpenSWATHtoMSstatsFormatImport OpenSWATH files
PDtoMSstatsFormatImport Proteome Discoverer files
ProgenesistoMSstatsFormatImport Progenesis files
quantificationProtein sample quantification or group quantification
savePlotSave a plot to pdf file
SDRFtoAnnotationConvert SDRF experimental design file into an MSstats...
SkylinetoMSstatsFormatImport Skyline files
SpectronauttoMSstatsFormatImport Spectronaut files
SRMRawDataExample dataset from a SRM experiment with stable isotope...
theme_msstatsTheme for MSstats plots
MeenaChoi/MSstats documentation built on June 1, 2024, 11:05 a.m.