# Automation and visualization of flow cytometry data analysis pipelines

## Documentation for package ‘CytoPipeline’ version 1.12.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

addProcessingStep | handling processing steps in CytoPipeline objects
aggregateAndSample | Aggregate and sample multiple flow frames of a flow set together
appendCellID | append 'Original_ID' column to a flowframe
applyScaleTransforms | apply scale transforms
areFluoCols | find flow frame columns that represent fluorochrome channel
areSignalCols | find flow frame columns that represent true signal
as.json.CytoProcessingStep | Cyto Processing step
as.list.CytoPipeline | CytoPipeline class
as.list.CytoProcessingStep | Cyto Processing step
buildCytoPipelineFromCache | interaction between CytoPipeline object and disk cache
characterOrFunction-class | Cyto Processing step
checkCytoPipelineConsistencyWithCache | interaction between CytoPipeline object and disk cache
cleanProcessingSteps | handling processing steps in CytoPipeline objects
collectNbOfRetainedEvents | inspect CytoPipeline results objects
compensateFromMatrix | compensation of fcs file(s) from matrix

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).

CytoPipeline-class | CytoPipeline class
CytoPipeline-class, | CytoPipeline class
CytoPipeline-method | CytoPipeline class
CytoPipelineClass | CytoPipeline class
CytoProcessingStep | Cyto Processing step
CytoProcessingStep-class | Cyto Processing step
deleteCytoPipelineCache | interaction between CytoPipeline object and disk cache
estimateScaleTransforms | estimates scale tranformations
execute | executing CytoPipeline object
executeProcessingStep | Cyto Processing step
experimentName | CytoPipeline class
experimentName<- | CytoPipeline class
export2JSONFile | exporting CytoPipeline objects
exportCytoPipeline | exporting CytoPipeline objects
findTimeChannel | find time channel in flowSet/flowFrame
from.json.CytoProcessingStep | Cyto Processing step
getAcquiredCompensationMatrix | extract compensation matrix from a flowCore::flowFrame
getChannelNamesFromMarkers | get channel names from markers
getCPSARGS | Cyto Processing step
getCPSFUN | Cyto Processing step
getCPSName | Cyto Processing step
getCytoPipelineExperimentNames | inspect CytoPipeline results objects
getCytoPipelineFlowFrame | inspect CytoPipeline results objects
getCytoPipelineObjectFromCache | inspect CytoPipeline results objects
getCytoPipelineObjectInfos | inspect CytoPipeline results objects
getCytoPipelineScaleTransform | inspect CytoPipeline results objects
getFCSFileName | get fcs file name
getNbProcessingSteps | handling processing steps in CytoPipeline objects
getProcessingStep | handling processing steps in CytoPipeline objects
getProcessingStepNames | handling processing steps in CytoPipeline objects
getTransfoParams | get tranformation parameters for a specific channel
ggplotEvents | plot events in 1D or 2D, using ggplot2
ggplotFilterEvents | plot filtered events in 2D, using ggplot
ggplotFlowRate | plot flow rate as a function of time, using ggplot2
handlingProcessingSteps | handling processing steps in CytoPipeline objects
inspectCytoPipelineObjects | inspect CytoPipeline results objects
interactingWithCytoPipelineCache | interaction between CytoPipeline object and disk cache
OMIP021Samples | OMIP021Samples dataset
pData | CytoPipeline class
pData<- | CytoPipeline class
plotCytoPipelineProcessingQueue | inspect CytoPipeline results objects
qualityControlFlowAI | perform QC with flowAI
qualityControlPeacoQC | perform QC with PeacoQC
readRDSObject | read RDS object
readSampleFiles | Read fcs sample files
removeChannels | remove channels from a flowFrame
removeDeadCellsManualGate | remove dead cells from a flowFrame using manual gating
removeDebrisManualGate | remove debris from a flowFrame using manual gating
removeDoubletsCytoPipeline | remove doublets from a flowFrame, using CytoPipeline custom algorithm
removeMarginsPeacoQC | remove margin events using PeacoQC
removeProcessingStep | handling processing steps in CytoPipeline objects
resetCellIDs | reset 'Original_ID' column in a flowframe
runCompensation | compensate with additional options
sampleDisplayNames | CytoPipeline class
sampleFiles | CytoPipeline class
sampleFiles<- | CytoPipeline class
sampleNameFromDisplayName | CytoPipeline class
show-method | CytoPipeline class
show-method | Cyto Processing step
showProcessingSteps | handling processing steps in CytoPipeline objects
singletsGate | Clean doublet events from flow cytometry data
subsample | sub-sampling of a flowFrame
updateMarkerName | update marker name of a given flowFrame channel
writeFlowFrame | write flowFrame to disk