Package index • GatingTree

All functions

CreateFlowObject(): Create FlowObject by importing flow cytometric data

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

FlowObject-class: A class representing a FlowObject object

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

PlotFlow2D(): Two-Dimensional Plot with Gating and Quadrant Statistics

PlotNodeScatterPlot(): Plot Node Scatter Plot

PlotNormAF(): Plot Effects of Autofluorescnce Modelling

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

SampleDef(): SampleDef

addChildNode(): Add a Child Node to a Gating Tree

collect_history(): Collect History from Gating Tree

collect_leaf_enrichment(): Collect Enrichment Data from Leaf Nodes

collect_markers(): Collect Markers from a Gating Tree

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

convert_to_diagrammer(): Convert Gating Tree to DiagrammeR Graph

createChildNode(): Create a Child Node in a Gating Tree

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

logSingleData(): Logarithmically Transforms a Vector

logTransformData(): Logarithmically Transforms Each Column of a Matrix

moderate_log_transform(): Moderately Log Transforms a Vector with Adjustments

recursiveAddChildNode(): Recursively Add Child Nodes in a Gating Tree

showSampleDef(): Show SampleDef