Package index • GatingTree

All functions

AnalyzeNodeOverlaps(): Analyze Cell Overlaps Between Nodes And Generate Heatmap

CreateFlowObject(): Create FlowObject by importing flow cytometric data

DefineNegatives(): Interactively determine gates to define negative (and positive) regions for each marker expression

ExtractGatingTree(): Extract and Finalize the Gating Tree Object

ExtractTopNodes(): Extract Top Nodes from Node Overlaps in a FlowObject

FlowObject-class: A class representing a FlowObject object

GatingTreeRandomForest(): Perform Random Forest Analysis Using GatingTree Node Data

GatingTreeToDF(): Convert Gating Tree Object to Data Frames

LogData(): Log fluorescence data

NormAF(): Moderate Extreme Negative Outliers with Random Values within Noise

PlotDefineNegatives(): Plot the threshold for for each marker expression as per determined by DefineNegatives

PlotDeltaEnrichment(): Plot Delta Enrichment or Interaction Effects for Each Marker

PlotDeltaEnrichmentPrunedTree(): Plot Delta Enrichment or Interaction Effects for Each Marker Using Pruned GatingTree

PlotNodeScatterPlot(): Plot Node Scatter Plot

PlotNormAF(): Plot Effects of Autofluorescnce Modelling

PruneGatingTree(): Prune a Gating Tree Based on Statistical Criteria

SampleDef(): SampleDef

convertGatingTreeToGraph(): Convert Gating Tree to Graphical Representation

convertToDataTree(): Convert Gating Tree Node to Data Tree Node

convert_to_diagrammer(): Convert Gating Tree to DiagrammeR Graph

createGatingTreeObject(): Create a Gating Tree Object

export_negative_gate_def(): Export Negative Gate Definitions from FlowObject

extractNodes(): Extract All Nodes from GatingTree

findNodeByPath(): Find a Node by Path in a Gating Tree

flowObject(): Create a new FlowObject

getNode(): Retrieve a Node from a Gating Tree

import_negative_gate_def(): Import Negative Gate Definitions into FlowObject

plotFlow2D(): Two-Dimensional Plot with Gating and Quadrant Statistics

predictGatingTreeRandomForest(): Predict Using GatingTreeRandomForest Model

showSampleDef(): Show SampleDef