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

## Documentation for package ‘ClustAll’ version 1.6.0

- 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