ClustAll: Data driven strategy to find groups of patients within complex diseases

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Documentation for package ‘ClustAll’ version 1.0.0

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

Help Pages

addValidationData	Add the validation data into the ClustAllObject
addValidationData-method	Add the validation data into the ClustAllObject
characterOrNA	characterOrNA Class union of character, null or missing
characterOrNA-class	characterOrNA Class union of character, null or missing
ClustAllObject-class	ClustAllObject
cluster2data	cluster2data
cluster2data-method	cluster2data
createClustAll	Creates ClustAllObject and perform imputations to deal with missing values
createClustAll-method	Creates ClustAllObject and perform imputations to deal with missing values
dataImputed	Retrieve the imputed data from ClustAllObject
dataImputed-method	Retrieve the imputed data from ClustAllObject
dataOriginal	Retrieve the initial dataOriginal from ClustAllObject
dataOriginal-method	Retrieve the initial dataOriginal from ClustAllObject
dataValidation	Retrieve the original data labelling from ClustAllObject
dataValidation-method	Retrieve the original data labelling from ClustAllObject
initialize-method	initializeClustAllObject
JACCARD_DISTANCE_F	Retrieve the matrix with the Jaccard distances derived from the robust populations stratifications in ClustAllObject
JACCARD_DISTANCE_F-method	Retrieve the matrix with the Jaccard distances derived from the robust populations stratifications in ClustAllObject
listOrNULL	Class Union listOrNULL
listOrNULL-class	Class Union listOrNULL
logicalOrNA	logicalOrNA
logicalOrNA-class	logicalOrNA
matrixOrNULL	matrixOrNULL
matrixOrNULL-class	matrixOrNULL
nImputation	Retrieve the number of imputations applied at the imputation step from ClustAllObject
nImputation-method	Retrieve the number of imputations applied at the imputation step from ClustAllObject
numericOrCharacter	numericOrCharacter
numericOrCharacter-class	numericOrCharacter
numericOrNA	Class Union numericOrNA
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	Correlation matrix heatmap showing the Jaccard distance between robust stratifications in the ClustAllObject
plotJACCARD-method	Correlation matrix heatmap showing the Jaccard distance between robust stratifications in the ClustAllObject
plotSANKEY	Plots Sankey Diagram showing the cluster distribution and shifts between a pair of stratifications derived from ClustAllObject
plotSANKEY-method	Plots Sankey Diagram showing the cluster distribution and shifts between a pair of stratifications derived from ClustAllObject
processed	Retrieve logical if runClustAll has been executed considering ClustAllObject as input
processed-method	Retrieve logical if runClustAll has been executed considering ClustAllObject as input
resStratification	Show the stratification representatives from the ClustAllObject
resStratification-method	Show the stratification representatives from the ClustAllObject
runClustAll	ClustAll: Data driven strategy to find hidden subgroups of patients within complex diseases using clinical data
runClustAll-method	ClustAll: Data driven strategy to find hidden subgroups of patients within complex diseases using clinical data
show-method	show method for ClustAllObject
showData	Retrieve the initial data from ClustAllObject
showData-method	Retrieve the initial data from ClustAllObject
summary_clusters	Retrieve the resulting stratifications for each combination of clusterings method (distance + clustering algorithm) and depth from ClustAllObject
summary_clusters-method	Retrieve the resulting stratifications for each combination of clusterings method (distance + clustering algorithm) and depth from ClustAllObject
validateStratification	validateStratification
validateStratification-method	validateStratification
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