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

## Documentation for package ‘IRISFGM’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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