Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

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Documentation for package ‘IRISFGM’ version 1.8.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G I K L M P Q R S misc

-- A --

AddMeta	AddMeta
AddMeta-method	AddMeta

-- B --

BIC_LTMG	BIC_LTMG BIC_LTMG
BIC_ZIMG	BIC_ZIMG fits different model BIC_ZIMG fits different model

-- C --

CalBinaryMultiSignal	CalBinaryMultiSignal
CalBinaryMultiSignal-method	CalBinaryMultiSignal
CalBinarySingleSignal	CalBinarySingleSignal
CalBinarySingleSignal-method	CalBinarySingleSignal
CLUSTERING	Packaging clustering method This function is used for choosing clustering method
CreateIRISFGMObject	CreateIRISFGMObject

-- D --

DimReduce-class	Create DimReduce object
DotPlotPathway	DotPlotPathway
DotPlotPathway-method	DotPlotPathway

-- E --

example_object

Example object.

-- F --

FindClassBasedOnMC	FindClassBasedOnMC
FindClassBasedOnMC-method	FindClassBasedOnMC
FindGlobalMarkers	FindGlobalMarkers
FindGlobalMarkers-method	FindGlobalMarkers
FindMarker	FindMarker
FindMarker-method	FindMarker
Fit_LTMG	Fit_LTMG Fit_LTMG

-- G --

GetBinaryMultiSignal	GetBinaryMultiSignal
GetBinaryMultiSignal-method	GetBinaryMultiSignal
GetBinarySingleSignal	GetBinarySingleSignal
GetBinarySingleSignal-method	GetBinarySingleSignal
GetLTMGmatrix	GetLTMGmatrix
GetLTMGmatrix-method	GetLTMGmatrix
getMeta	getMeta
getMeta-method	getMeta
Global_Zcut	Global_Zcut create Zcut Global_Zcut create Zcut
GRAPH	generate graph

-- I --

InverseMillsRatio	Title Title
IRISFGM-class	IRISFGM

-- K --

KS_LTMG	KS_LTMG KS_LTMG
KS_ZIMG	KS_ZIMG KS_ZIMG

-- L --

LogSeparateKRpkmNew	Title Title
LogSeparateKRpkmNewLR	LogSeparateKRpkmNewLR
LTMG	LTMG LTMG

-- M --

MCL	MCL clustering MCL clustering
MINUS	MINUS MINUS
MIN_return	MIN_return MIN_return

-- P --

Pi_Zj_Zcut_new	Pi_Zj_Zcut_new Pi_Zj_Zcut_new
PlotDimension	PlotDimension
PlotDimension-method	PlotDimension
PlotHeatmap	PlotHeatmap
PlotHeatmap-method	PlotHeatmap
PlotMarkerHeatmap	PlotMarkerHeatmap will visualize global marker This function will generate global marker gene heatmap
PlotMeta	PlotMeta
PlotMeta-method	PlotMeta
PlotModuleNetwork	PlotModuleNetwork
PlotModuleNetwork-method	PlotModuleNetwork
PlotNetwork	PlotNetwork
PlotNetwork-method	PlotNetwork
ProcessData	ProcessData
ProcessData-method	ProcessData
Pure_CDF	Pure_CDF Pure_CDF

-- Q --

qubic

qubic

-- R --

ReadFrom10X_folder	ReadFrom10X_folder
ReadFrom10X_folder-method	ReadFrom10X_folder
ReadFrom10X_h5	ReadFrom10X_h5
ReadFrom10X_h5-method	ReadFrom10X_h5
RunBicluster	RunBicluster
RunBicluster-method	RunBicluster
RunClassification	RunClassification
RunClassification-method	RunClassification
RunDimensionReduction	RunDimensionReduction
RunDimensionReduction-method	RunDimensionReduction
RunDiscretization	RunDiscretization
RunDiscretization-method	RunDiscretization
RunLTMG	RunLTMG
RunLTMG-method	RunLTMG
RunPathway	RunPathway
RunPathway-method	RunPathway

-- S --

SC	spectral Clustering method spectral Clustering method
SeparateKRpkmNew	SeparateKRpkmNew SeparateKRpkmNew
SeparateKRpkmNew2	SeparateKRpkmNew2 SeparateKRpkmNew2
SeparateKRpkmNewLR	SeparateKRpkmNewLRPlus Calcuate the LTMG_2LR for some genes Calcuate the LTMG_2LR for some genes
SeparateKRpkmNewLRPlus	SeparateKRpkmNewLRPlus Calcuate the LTMG_2LR for some genes Calcuate the LTMG_2LR for some genes
SeparateKRpkmNewp	Title Title
State_return	State_return State_return
SubsetData	SubsetData
SubsetData-method	SubsetData

-- misc --

.addMeta	AddMeta
.CalBinaryMultiSignal	CalBinaryMultiSignal
.CalBinarySingleSignal	CalBinarySingleSignal
.dotPlotPathway	DotPlotPathway
.final	FindClassBasedOnMC
.findglobalMarkers	FindGlobalMarkers
.findMarker	FindMarker
.generateNetObject	GenerateNetObject Generate Net Object for the network use.
.GetBinaryMultiSignal	GetBinaryMultiSignal
.GetBinarySingleSignal	GetBinarySingleSignal
.getBlock	getblock function
.GetLTMGmatrix	GetLTMGmatrix
.getmeta	getMeta
.IDConvert	convert ID convert ID
.plotDimension	PlotDimension
.plotHeatmap	PlotHeatmap
.plotMeta	PlotMeta
.plotmodulenetwork	PlotModuleNetwork
.processData	ProcessData
.runBicluster	RunBicluster
.runBiclusterBaseOnDiscretization	Run Discretization Generate temporal discretized file
.runBiclusterBaseOnLTMG	RunBicusterBaseOnLTMG
.runClassification	RunClassification
.runDimensionReduction	RunDimensionReduction
.runDiscretization	RunDiscretization
.RunGO	RunGO RunGO
.RunKEGG	RunKEGG RunKEGG
.RunLTMG	RunLTMG
.runPathway	RunPathway
.separateBic	separateBic separate biclusters
.subset_data	SubsetData