COexpression Tables ANalysis


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Documentation for package ‘COTAN’ version 2.7.4

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A B C D E F G H I L M N O P R S T U V

-- A --

addClusterization Handling cells' _clusterization_ and related functions
addClusterization-method Handling cells' _clusterization_ and related functions
addClusterizationCoex Handling cells' _clusterization_ and related functions
addClusterizationCoex-method Handling cells' _clusterization_ and related functions
addCondition Handling cells' _conditions_ and related functions
addCondition-method Handling cells' _conditions_ and related functions
addElementToMetaDataset Handling _meta-data_ in 'COTAN' objects
addElementToMetaDataset-method Handling _meta-data_ in 'COTAN' objects
AdvancedGDIUniformityCheck-class Definition of the *Transcript Uniformity Checker* classes
asClusterization _Clusters_ utilities
automaticCOTANObjectCreation 'COTAN' shortcuts

-- B --

BaseUniformityCheck-class Definition of the *Transcript Uniformity Checker* classes

-- C --

calculateCoex Calculating the COEX matrix for genes and cells
calculateCoex-method Calculating the COEX matrix for genes and cells
calculateG Calculating the COEX matrix for genes and cells
calculateGDI Calculations of genes statistics
calculateGDIGivenCorr Calculations of genes statistics
calculateGenesCE Calculations of genes statistics
calculateLikelihoodOfObserved Calculating the COEX matrix for genes and cells
calculateMu Calculating the COEX matrix for genes and cells
calculatePartialCoex Calculating the COEX matrix for genes and cells
calculatePDI Calculations of genes statistics
calculatePValue Calculations of genes statistics
calculateS Calculating the COEX matrix for genes and cells
calculateThresholdShiftToUniformity Definition of the *Transcript Uniformity Checker* classes
calculateThresholdShiftToUniformity-method Definition of the *Transcript Uniformity Checker* classes
CalculatingCOEX Calculating the COEX matrix for genes and cells
canUseTorch Handling Multi-Core and GPU environments
cellsHeatmapPlot Heatmap Plots
cellSizePlot Raw data cleaning
cellsUMAPPlot Handling cells' _clusterization_ and related functions
cellsUniformClustering Uniform Clusters
checkClusterUniformity Uniform Clusters
checkersToDF Definition of the *Transcript Uniformity Checker* classes
checkObjIsUniform Definition of the *Transcript Uniformity Checker* classes
checkObjIsUniform-method Definition of the *Transcript Uniformity Checker* classes
clean Raw data cleaning
clean-method Raw data cleaning
cleanPlots Raw data cleaning
clusterGeneContingencyTables Handling cells' _clusterization_ and related functions
clustersDeltaExpression Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
ClustersList _Clusters_ utilities
clustersMarkersHeatmapPlot Handling cells' _clusterization_ and related functions
clustersSummaryData Handling cells' _clusterization_ and related functions
clustersSummaryPlot Handling cells' _clusterization_ and related functions
clustersTreePlot Handling cells' _clusterization_ and related functions
conditionsFromNames Handle names and factors' levels
contingencyTables Calculating the COEX matrix for genes and cells
Conversions Data class conversions
convertFromSingleCellExperiment Data class conversions
convertToSingleCellExperiment Data class conversions
COTAN 'COTAN' shortcuts
COTAN-class Definition of the 'COTAN' class
COTAN_coerce_to_scCOTAN Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
COTAN_Legacy Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
COTAN_ObjectCreation 'COTAN' shortcuts

-- D --

Datasets Data-sets
datasetTags Handling _meta-data_ in 'COTAN' objects
DEAOnClusters Handling cells' _clusterization_ and related functions
dfToCheckers Definition of the *Transcript Uniformity Checker* classes
dispersionBisection Numeric Utilities
distancesBetweenClusters Handling cells' _clusterization_ and related functions
dropCellsCoex Calculating the COEX matrix for genes and cells
dropCellsCoex-method Calculating the COEX matrix for genes and cells
dropClusterization Handling cells' _clusterization_ and related functions
dropClusterization-method Handling cells' _clusterization_ and related functions
dropCondition Handling cells' _conditions_ and related functions
dropCondition-method Handling cells' _conditions_ and related functions
dropGenesCells Raw data cleaning
dropGenesCells-method Raw data cleaning
dropGenesCoex Calculating the COEX matrix for genes and cells
dropGenesCoex-method Calculating the COEX matrix for genes and cells

-- E --

ECDPlot Raw data cleaning
ERCCraw Data-sets
establishGenesClusters Calculations of genes statistics
estimateDispersionBisection Estimation of the 'COTAN' model's parameters
estimateDispersionBisection-method Estimation of the 'COTAN' model's parameters
estimateDispersionNuBisection Estimation of the 'COTAN' model's parameters
estimateDispersionNuBisection-method Estimation of the 'COTAN' model's parameters
estimateDispersionNuNlminb Estimation of the 'COTAN' model's parameters
estimateDispersionNuNlminb-method Estimation of the 'COTAN' model's parameters
estimateLambdaLinear Estimation of the 'COTAN' model's parameters
estimateLambdaLinear-method Estimation of the 'COTAN' model's parameters
estimateNuBisection Estimation of the 'COTAN' model's parameters
estimateNuBisection-method Estimation of the 'COTAN' model's parameters
estimateNuLinear Estimation of the 'COTAN' model's parameters
estimateNuLinear-method Estimation of the 'COTAN' model's parameters
estimateNuLinearByCluster Handling cells' _clusterization_ and related functions
estimateNuLinearByCluster-method Handling cells' _clusterization_ and related functions
estimatorsAreReady Estimation of the 'COTAN' model's parameters
expectedContingencyTables Calculating the COEX matrix for genes and cells
expectedContingencyTablesNN Calculating the COEX matrix for genes and cells
expectedPartialContingencyTables Calculating the COEX matrix for genes and cells
expectedPartialContingencyTablesNN Calculating the COEX matrix for genes and cells

-- F --

factorToVector Handle names and factors' levels
findClustersMarkers Handling cells' _clusterization_ and related functions
findFullyExpressedGenes Raw data cleaning
findFullyExpressedGenes-method Raw data cleaning
findFullyExpressingCells Raw data cleaning
findFullyExpressingCells-method Raw data cleaning
flagNotFullyExpressedGenes Raw data cleaning
flagNotFullyExpressedGenes-method Raw data cleaning
flagNotFullyExpressingCells Raw data cleaning
flagNotFullyExpressingCells-method Raw data cleaning
fromClustersList _Clusters_ utilities
funProbZero Numeric Utilities

-- G --

GDICheck-class Definition of the *Transcript Uniformity Checker* classes
GDIPlot Uniform Clusters
genesCoexSpace Calculations of genes statistics
geneSetEnrichment Handling cells' _clusterization_ and related functions
genesHeatmapPlot Heatmap Plots
genesSizePlot Raw data cleaning
GenesStatistics Calculations of genes statistics
getAllConditions Handling cells' _conditions_ and related functions
getAllConditions-method Handling cells' _conditions_ and related functions
getCells Raw data 'COTAN' accessors
getCells-method Raw data 'COTAN' accessors
getCellsCoex Calculating the COEX matrix for genes and cells
getCellsCoex-method Calculating the COEX matrix for genes and cells
getCellsSize Raw data 'COTAN' accessors
getCellsSize-method Raw data 'COTAN' accessors
getCheckerThreshold Definition of the *Transcript Uniformity Checker* classes
getCheckerThreshold-method Definition of the *Transcript Uniformity Checker* classes
getClusterizationData Handling cells' _clusterization_ and related functions
getClusterizationData-method Handling cells' _clusterization_ and related functions
getClusterizationName Handling cells' _clusterization_ and related functions
getClusterizationName-method Handling cells' _clusterization_ and related functions
getClusterizations Handling cells' _clusterization_ and related functions
getClusterizations-method Handling cells' _clusterization_ and related functions
getClusters Handling cells' _clusterization_ and related functions
getClustersCoex Handling cells' _clusterization_ and related functions
getClustersCoex-method Handling cells' _clusterization_ and related functions
getColorsVector getColorsVector
getColumnFromDF Handling _meta-data_ in 'COTAN' objects
getCondition Handling cells' _conditions_ and related functions
getCondition-method Handling cells' _conditions_ and related functions
getConditionName Handling cells' _conditions_ and related functions
getConditionName-method Handling cells' _conditions_ and related functions
getDims Handling _meta-data_ in 'COTAN' objects
getDims-method Handling _meta-data_ in 'COTAN' objects
getDispersion Estimation of the 'COTAN' model's parameters
getDispersion-method Estimation of the 'COTAN' model's parameters
getFullyExpressedGenes Raw data cleaning
getFullyExpressedGenes-method Raw data cleaning
getFullyExpressingCells Raw data cleaning
getFullyExpressingCells-method Raw data cleaning
getGDI Calculations of genes statistics
getGDI-method Calculations of genes statistics
getGenes Raw data 'COTAN' accessors
getGenes-method Raw data 'COTAN' accessors
getGenesCoex Calculating the COEX matrix for genes and cells
getGenesCoex-method Calculating the COEX matrix for genes and cells
getGenesSize Raw data 'COTAN' accessors
getGenesSize-method Raw data 'COTAN' accessors
getLambda Estimation of the 'COTAN' model's parameters
getLambda-method Estimation of the 'COTAN' model's parameters
getLogNormData Estimation of the 'COTAN' model's parameters
getMetadataCells Handling _meta-data_ in 'COTAN' objects
getMetadataCells-method Handling _meta-data_ in 'COTAN' objects
getMetadataDataset Handling _meta-data_ in 'COTAN' objects
getMetadataDataset-method Handling _meta-data_ in 'COTAN' objects
getMetadataElement Handling _meta-data_ in 'COTAN' objects
getMetadataElement-method Handling _meta-data_ in 'COTAN' objects
getMetadataGenes Handling _meta-data_ in 'COTAN' objects
getMetadataGenes-method Handling _meta-data_ in 'COTAN' objects
getMu Calculating the COEX matrix for genes and cells
getNormalizedData Estimation of the 'COTAN' model's parameters
getNu Estimation of the 'COTAN' model's parameters
getNu-method Estimation of the 'COTAN' model's parameters
getNumCells Raw data 'COTAN' accessors
getNumCells-method Raw data 'COTAN' accessors
getNumExpressedGenes Raw data 'COTAN' accessors
getNumExpressedGenes-method Raw data 'COTAN' accessors
getNumGenes Raw data 'COTAN' accessors
getNumGenes-method Raw data 'COTAN' accessors
getNumOfExpressingCells Raw data 'COTAN' accessors
getNumOfExpressingCells-method Raw data 'COTAN' accessors
getNuNormData Estimation of the 'COTAN' model's parameters
getProbabilityOfZero Estimation of the 'COTAN' model's parameters
getRawData Raw data 'COTAN' accessors
getRawData-method Raw data 'COTAN' accessors
getZeroOneProj Raw data 'COTAN' accessors
getZeroOneProj-method Raw data 'COTAN' accessors
groupByClusters _Clusters_ utilities
groupByClustersList _Clusters_ utilities

-- H --

HandleMetaData Handling _meta-data_ in 'COTAN' objects
handleMultiCore Handling Multi-Core and GPU environments
handleNamesSubsets Handle names and factors' levels
HandleStrings Handle names and factors' levels
HandlingClusterizations Handling cells' _clusterization_ and related functions
HandlingConditions Handling cells' _conditions_ and related functions
heatmapPlot Heatmap Plots
HeatmapPlots Heatmap Plots

-- I --

initializeMetaDataset Handling _meta-data_ in 'COTAN' objects
initializeMetaDataset-method Handling _meta-data_ in 'COTAN' objects
Installing_torch Installing torch R library (on Linux)
isCoexAvailable Calculating the COEX matrix for genes and cells
isCoexAvailable-method Calculating the COEX matrix for genes and cells
isEmptyName Handle names and factors' levels

-- L --

logFoldChangeOnClusters Handling cells' _clusterization_ and related functions
LoggingFunctions Logging in the 'COTAN' package
logThis Logging in the 'COTAN' package

-- M --

mat2vec_rfast Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
mergeClusters _Clusters_ utilities
mergeUniformCellsClusters Uniform Clusters
mitochondrialPercentagePlot Raw data cleaning
multiMergeClusters _Clusters_ utilities
MultiThreading Handling Multi-Core and GPU environments

-- N --

niceFactorLevels Handle names and factors' levels
normalizeNameAndLabels Handling cells' _conditions_ and related functions
nuBisection Numeric Utilities
NumericUtilities Numeric Utilities

-- O --

observedContingencyTables Calculating the COEX matrix for genes and cells
observedContingencyTablesYY Calculating the COEX matrix for genes and cells
observedPartialContingencyTables Calculating the COEX matrix for genes and cells
observedPartialContingencyTablesYY Calculating the COEX matrix for genes and cells

-- P --

parallelDispersionBisection Numeric Utilities
parallelNuBisection Numeric Utilities
ParametersEstimations Estimation of the 'COTAN' model's parameters
plotTheme Heatmap Plots
proceedToCoex 'COTAN' shortcuts
proceedToCoex-method 'COTAN' shortcuts
pValueFromDEA Handling cells' _clusterization_ and related functions

-- R --

raw.dataset Data-sets
RawDataCleaning Raw data cleaning
RawDataGetters Raw data 'COTAN' accessors
reorderClusterization Handling cells' _clusterization_ and related functions

-- S --

scatterPlot Raw data cleaning
scCOTAN-class Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
scCotan_coerce_to_COTAN Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
screePlot Raw data cleaning
setColumnInDF Handling _meta-data_ in 'COTAN' objects
setLoggingFile Logging in the 'COTAN' package
setLoggingLevel Logging in the 'COTAN' package
shiftCheckerThresholds Definition of the *Transcript Uniformity Checker* classes
shiftCheckerThresholds-method Definition of the *Transcript Uniformity Checker* classes
SimpleGDIUniformityCheck-class Definition of the *Transcript Uniformity Checker* classes
singleHeatmapDF Heatmap Plots
storeGDI Calculations of genes statistics
storeGDI-method Calculations of genes statistics

-- T --

test.dataset Data-sets
test.dataset.clusters1 Data-sets
test.dataset.clusters2 Data-sets
toClustersList _Clusters_ utilities

-- U --

UMAPPlot Handling cells' _clusterization_ and related functions
UniformClusters Uniform Clusters
UniformTranscriptCheckers Definition of the *Transcript Uniformity Checker* classes

-- V --

vec2mat_rfast Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions
vignette.merge.clusters Data-sets
vignette.merge2.clusters Data-sets
vignette.split.clusters Data-sets