Package index
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show(<CytoPipeline>)CytoPipeline(<missing>)CytoPipeline(<list>)CytoPipeline(<character>)as.list(<CytoPipeline>)experimentName()`experimentName<-`()sampleFiles()`sampleFiles<-`()pData()`pData<-`() - CytoPipeline class
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CytoProcessingStep()show(<CytoProcessingStep>)executeProcessingStep()getCPSName()getCPSFUN()getCPSARGS()as.list(<CytoProcessingStep>)as.json.CytoProcessingStep()from.json.CytoProcessingStep() - Cyto Processing step
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OMIP021Samples - OMIP021Samples dataset
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aggregateAndSample() - Aggregate and sample multiple flow frames of a flow set together
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appendCellID() - append 'Original_ID' column to a flowframe
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applyScaleTransforms() - apply scale transforms
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areFluoCols() - find flow frame columns that represent fluorochrome channel
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areSignalCols() - find flow frame columns that represent true signal
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compensateFromMatrix() - compensation of fcs file(s) from matrix
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computeScatterChannelsLinearScale() - compute linear transformation of scatter channels found in ff, based on 5% and 95% of referenceChannel, set as target. If there is a transformation defined in transList for referenceChannel, it is applied first, before computing quantiles. Then the computed linear transformations (or each scatter channel) are added into the transfo_list. -A channels are computed, and same linear transformation is then applied to corresponding -W and -H channels (if they exist in ff).
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estimateScaleTransforms() - estimates scale tranformations
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execute() - executing CytoPipeline object
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export2JSONFile() - exporting CytoPipeline objects
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findTimeChannel() - find time channel in flowSet/flowFrame
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getAcquiredCompensationMatrix() - extract compensation matrix from a flowCore::flowFrame
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getChannelNamesFromMarkers() - get channel names from markers
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getFCSFileName() - get fcs file name
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getTransfoParams() - get tranformation parameters for a specific channel
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ggplotEvents() - plot events in 1D or 2D, using ggplot2
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ggplotFilterEvents() - plot filtered events in 2D, using ggplot
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ggplotFlowRate() - plot flow rate as a function of time, using ggplot2
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addProcessingStep()removeProcessingStep()getNbProcessingSteps()getProcessingStep()getProcessingStepNames()cleanProcessingSteps()showProcessingSteps() - handling processing steps in CytoPipeline objects
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getCytoPipelineExperimentNames()getCytoPipelineObjectFromCache()getCytoPipelineObjectInfos()getCytoPipelineFlowFrame()getCytoPipelineScaleTransform()plotCytoPipelineProcessingQueue()collectNbOfRetainedEvents() - inspect CytoPipeline results objects
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deleteCytoPipelineCache()buildCytoPipelineFromCache()checkCytoPipelineConsistencyWithCache() - interaction between CytoPipeline object and disk cache
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qualityControlFlowAI() - perform QC with flowAI
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qualityControlPeacoQC() - perform QC with PeacoQC
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readRDSObject() - read RDS object
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readSampleFiles() - Read fcs sample files
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removeChannels() - remove channels from a flowFrame
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removeDeadCellsManualGate() - remove dead cells from a flowFrame using manual gating
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removeDebrisManualGate() - remove debris from a flowFrame using manual gating
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removeDoubletsCytoPipeline() - remove doublets from a flowFrame, using CytoPipeline custom algorithm
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removeMarginsPeacoQC() - remove margin events using PeacoQC
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resetCellIDs() - reset 'Original_ID' column in a flowframe
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runCompensation() - compensate with additional options
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singletsGate() - Clean doublet events from flow cytometry data
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subsample() - sub-sampling of a flowFrame
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updateMarkerName() - update marker name of a given flowFrame channel
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writeFlowFrame() - write flowFrame to disk