ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

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Documentation for package ‘ClustAll’ version 1.4.0

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

Help Pages

addValidationData	Add Validation Data to ClustAllObject
addValidationData-method	Add Validation Data to ClustAllObject
characterOrNA-class	Class Union: characterOrNA
ClustAllObject-class	ClustAllObject
cluster2data	Export Stratification Results with Original Data
cluster2data-method	Export Stratification Results with Original Data
createClustAll	Create ClustAllObject for Patient Stratification Analysis
createClustAll-method	Create ClustAllObject for Patient Stratification Analysis
dataImputed	Retrieve Imputed Data from ClustAllObject
dataImputed-method	Retrieve Imputed Data from ClustAllObject
dataOriginal	Retrieve Original Unprocessed Data from ClustAllObject
dataOriginal-method	Retrieve Original Unprocessed Data from ClustAllObject
dataValidation	Retrieve Validation Data from ClustAllObject
dataValidation-method	Retrieve Validation Data from ClustAllObject
extractData	extractData
extractData-method	extractData
extractResults	Extract Clustering Results from ClustAllObject
extractResults-method	Extract Clustering Results from ClustAllObject
heart_data	Heart Disease Dataset
initialize-method	initializeClustAllObject
JACCARD_DISTANCE_F	Retrieve Jaccard Distance Matrix for Robust Stratifications
JACCARD_DISTANCE_F-method	Retrieve Jaccard Distance Matrix for Robust Stratifications
listOrNULL-class	Class Union: listOrNULL
logicalOrNA-class	Class Union: logicalOrNA
matrixOrNULL-class	Class Union: matrixOrNULL
nImputation	Retrieve Number of Imputations from ClustAllObject
nImputation-method	Retrieve Number of Imputations from ClustAllObject
numericOrCharacter	Class Union: numericOrCharacter
numericOrCharacter-class	Class Union: numericOrCharacter
numericOrNA-class	Class Union: numericOrNA
obj_noNA1	obj_noNA1: Processed wdbc dataset for testing purposed
obj_noNA1simplify	obj_noNA1simplify: Processed wdbc dataset for testing purposed
obj_noNAno1Validation	obj_noNAno1Validation: Processed wdbc dataset for testing purposed
plotJACCARD	Visualize Jaccard Distances Between Robust Stratifications
plotJACCARD-method	Visualize Jaccard Distances Between Robust Stratifications
plotSANKEY	Visualize Stratification Comparisons with Sankey Diagram
plotSANKEY-method	Visualize Stratification Comparisons with Sankey Diagram
processed	Check Processing Status of ClustAllObject
processed-method	Check Processing Status of ClustAllObject
resStratification	Extract Representative Stratifications from ClustAllObject
resStratification-method	Extract Representative Stratifications from ClustAllObject
runClustAll	Execute ClustALL Algorithm on a ClustAllObject
runClustAll-method	Execute ClustALL Algorithm on a ClustAllObject
show-method	Display Summary of ClustAllObject
showData	Retrieve Processed Data from ClustAllObject
showData-method	Retrieve Processed Data from ClustAllObject
summary_clusters	Retrieve Summary of Clustering Results from ClustAllObject
summary_clusters-method	Retrieve Summary of Clustering Results from ClustAllObject
validateStratification	Validate Stratification Results Against True Labels
validateStratification-method	Validate Stratification Results Against True Labels
wdbc	wdbc: Diagnostic Wisconsin Breast Cancer Database.
wdbcMIDS	wdbcMIDS: Diagnostic Wisconsin Breast Cancer Database with imputed values
wdbcNA	wdbcNA: Diagnostic Wisconsin Breast Cancer Database with missing values