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


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Documentation for package ‘ClustAll’ version 1.0.1

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addValidationData addValidationData
addValidationData-method addValidationData
characterOrNA characterOrNA Class union of character, null and missing
characterOrNA-class characterOrNA Class union of character, null and missing
ClustAllObject-class ClustAllObject
cluster2data cluster2data: Export selected stratification(s)
cluster2data-method cluster2data: Export selected stratification(s)
createClustAll createClustAll: Creates ClustAllObject
createClustAll-method createClustAll: Creates ClustAllObject
dataImputed dataImputed accession method
dataImputed-method dataImputed accession method
dataOriginal dataOriginal accession method
dataOriginal-method dataOriginal accession method
dataValidation dataValidation accession method
dataValidation-method dataValidation accession method
extractData extractData
extractData-method extractData
extractResults extractResults
extractResults-method extractResults
initialize-method initializeClustAllObject
JACCARD_DISTANCE_F JACCARD_DISTANCE_F accession method
JACCARD_DISTANCE_F-method JACCARD_DISTANCE_F accession method
listOrNULL Class Union listOrNULL
listOrNULL-class Class Union listOrNULL
logicalOrNA logicalOrNA
logicalOrNA-class logicalOrNA
matrixOrNULL matrixOrNULL
matrixOrNULL-class matrixOrNULL
nImputation nImputation accession method
nImputation-method nImputation accession method
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 plotJACCARD: Heatmap of robust stratification distances based on Jaccard similarity
plotJACCARD-method plotJACCARD: Heatmap of robust stratification distances based on Jaccard similarity
plotSANKEY plotSANKEY: Plots Sankey Diagram showing the cluster distribution and shifts between a pair of stratifications derived from ClustAllObject
plotSANKEY-method plotSANKEY: Plots Sankey Diagram showing the cluster distribution and shifts between a pair of stratifications derived from ClustAllObject
processed processed accession method
processed-method processed accession method
resStratification resStratification: Show the representative stratifications
resStratification-method resStratification: Show the representative stratifications
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 data accession method
showData-method data accession method
summary_clusters summary_clusters accession method
summary_clusters-method summary_clusters accession method
validateStratification validateStratification: calculates the sensitivity and specificity of selected stratification
validateStratification-method validateStratification: calculates the sensitivity and specificity of selected stratification
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