# Pancreatic Ductal Adenocarcinoma Tool-Kit

## Documentation for package ‘PDATK’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

## -- A --

assignColDataColumn | assignColDataColumn Assign a new column directly to the colData slot of a SummarizedExperiment.
assignSubtypes | Assign Sample Subtypes to an S4 Object
assignSubtypes-method | Assign Subtype Annotations to a SurvivalExperiment Object
assignSubtypes-method | Assign Subtype Annotations to a SurvivalExperiment Object

## -- B --

barPlotModelComparison | Make A Bar Plot Comparing Performance Between Two 'S4' Objects Representing Mathematical Models.
barPlotModelComparison-method | Make a Bar Plot Comparison Model Performance Between a ClinicalModel and a PCOSP, RLSModel or RGAModel object.
birnbaum | Published classifier gene signature for Birnbaum

## -- C --

chen | Published classifier gene signature for Chen
ClinicalModel | Constructor for the ClinicalModel Class
ClinicalModel-class | ClinicalModel Class Definition
CohortList | Constructor for the CohortList class, a specialized list for storing SurvivalExperiment objects.
CohortList-class | CohortList Class Definition
cohortSubtypeDFs | A list of sample subtypes for the data in sampleCohortList
compareModels | Compare Two Mathematical Models Represented as 'S4' Objects
compareModels-method | Compare Two 'SurivalModel' Objects, Returing A 'ModelComparison' Object With Statistics Comparing the Performance of Each Model.
compareModels-method | Compare Two 'SurivalModel' Objects, Returing A 'ModelComparison' Object With Statistics Comparing the Performance of Each Model.
ConMetaclustModel | Constructor for a 'ConsensusClusterModel' Object.
ConsensusMetaclusteringModel | Constructor for a 'ConsensusClusterModel' Object.
ConsensusMetaclusteringModel-class | An 'S4Model' Containing Molecular Data to be Consensus Clustered
CoxModel | CoxModel constructor
CSPC_MAE | A 'MultiAssayExperiment' containing cohorts of pancreatic cancer patients, for use in package examples.

## -- D --

densityPlotModelComparison | Render A Density Plot of Model Performance for an 'S4' Object
densityPlotModelComparison-method | Render a Density Plot Comparing Model Performance Between Two 'PCOSP', 'RLSModel' or 'RGAModel' object.
dropNotCensored | Remove Censored Patient Samples from An 'S4' Object.
dropNotCensored-method | Remove Censored Patients from Each 'SurvivalExperiemnt' in a 'CohortList'
dropNotCensored-method | Remove Censored Patients from A 'SurvivalExperiment' Object

## -- E --

existingClassifierData | existingClassifierData

## -- F --

findCommonGenes | Find the common genes in an 'S4' object.
findCommonGenes-method | Intersect Gene Names for All 'SurvivalExperiments' in a 'CohortList'
findCommonGenes-method | Intersect Gene Names for All 'experiments' in a 'MultiAssayExperiment'
findCommonSamples | Find Common Samples in a List-like S4 Object where The Columns of Each Item Represent Samples
findCommonSamples-method | Find Common Samples in a CohortList Object where The Columns of Each Item Represent Samples
forestPlot | Generate a forest plot from an 'S4' object
forestPlot-method | Render a forest plot from the 'validationStats' slot of a 'PCOSP' model object.
forestPlot-method | Render a forest plot from the 'validationStats' slot of a 'PCOSP' model object.

## -- G --

GeneFuModel | 'GeneFuModel' Constructor Method
GeneFuModel-class | A 'SurvivalModel' Sub-class Designed to Hold A Survival Model Generated Using the 'genefu' R package.
getModelSeed | Generic for retrieving the randomSeed parameter from a 'SurvivalModel' object.
getModelSeed-method | Method for retrieving the random seed used for training a specific survival model object.
getTopFeatures | Get the Top Predictive Features from an S4 Object
getTopFeatures-method | Get the Top Ranked Features in a 'MultiAssayExperiment' object
getTopFeatures-method | Get the top features for classification using a PCOSP model object.
getTopFeatures-method | Get the Top Ranked Features in a 'SummarizedExperiment' object

## -- H --

haiderSigScores | Classifier survival scores for Haider
hasColDataColumns | Check for Column Names in the colData Slot of a SummarizedExperiment

## -- M --

merge-method | Merge two 'SurvivalExperiments', subsetting to shared rows and columns
ModelComparison | ModelComparison Constructor
ModelComparison-class | ModelComparison Class Definition
modelParams | Generic for Accessing the Model Parameters of an 'S4' Object
modelParams-method | Accessor for the Model Parameters of an 'S4Model' Object
models | Accessor for the models slot of an 'S4' object
models-method | Getter for the models slot of an 'S4Model' Object
models-method | Getter for the models slot of a 'SurvivalModel' object
models<--method | Setter for the models slot of a 'SurvivalModel' object

## -- N --

NCSModel | Constructor for a NetworkCommunitySearchModel (NCSModel)
NCSModel-class | S4Model Class for Metaclustering Using Network Community Search
NetworkCommunitySearchModel | Constructor for a NetworkCommunitySearchModel (NCSModel)
normalize-method | Normalize a S4 'DFrame' Object
normalize-method | Normalize the 'assays' of a 'MutliAssayExperiment' Object
normalize-method | Normalize the 'assays' in a 'SummarizedExperiment' Object
normalize-method | Normalize a 'data.frame' Object
normalsMAE | A 'MultiAssayExperiment' containing cohorts of normal patients, for package examples.

## -- O --

optimalKMinimizeAmbiguity | Predict optimal K values by minimizing the difference between the ECDF of clustering consensus at two points in a subinterval.

## -- P --

PCOSP | Pancreatic Cancer Overall Survival Predictor (PCOSP) Constructor
PCOSP-class | Pancreatic Cancer Overall Survival Predictor (PCOSP) Class
PCOSP_or_ClinicalModel-class | Class Union for PCOSP and ClinicalModel Types
PCOSP_or_RLS_or_RGA-class | Class Union for PCOSP, RLSModel and RGAModel Types
plotNetworkGraph | A Generic for Plotting a Network Graph From an S4 Object
plotNetworkGraph-method | Plot a Network Graph for a Classified NCSModel Object
plotROC | Plot ROC curves for an 'S4' object
plotROC-method | Plot ROC curves for a 'PCOSP' model object.
plotSurvivalCurves | Generic for Plotting Survival Curves from an 'S4' Object
plotSurvivalCurves-method | Plot Survival Curves from a Fit 'CoxModel' Object
predictClasses | Predict Classes for New Data Based on a Train Classifier Model
predictClasses-method | Use a Clinical GLM to Predict Classes for a 'CohortList' of 'SurvivalExperment' Objects.
predictClasses-method | Use a Gene Signature Based Prediciton Model from the 'genefu' Package to Predict Signature Scores for Each Sample
predictClasses-method | Predict Survival Prognosis Classes and Risk Scores for A 'CohortList' Using a 'PCOSP', 'RLSModel' or 'RGAModel' object.
predictClasses-method | Compute the Optimal Clustering Solution for a Trained ConsensusMetaclusteringModel
predictClasses-method | Predict Metacluster Labels for a NetworkCommunitySearchModel
predictClasses-method | Predict Survival Prognosis Classes and Risk Scores for A 'SurvivalModel' Using a 'ClinicalModel' Object.
predictClasses-method | Use a Gene Signature Based Prediciton Model from the 'genefu' Package to Predict Signature Scores for Each Sample.
predictClasses-method | Predict Survival Prognosis Classes and Risk Scores for A 'CohortList' Using a 'PCOSP', 'RLSModel' or 'RGAModel' object.
preprocessCaret | Preprocess Data Using the 'caret::preProcess' method, then return the normalized data using 'predict'.

## -- R --

RandomGeneAssignmentModel | RandomGeneAssignmentModel Constructor
RandomLabelShufflingModel | RandomLabelShufflingModel Constructor
rankFeatures | Rank the Features in a 'S4' Object
rankFeatures-method | Rank the Features in a 'MultiAssayExperiment' Object
rankFeatures-method | Rank the Features in a 'SummarizedExperiment' Object
removeColDataFactorColumns | Remave any factor columns from the 'colData' of an 'S4' object
removeFactorColumns | Convert factor columns in a rectangular object
renameColDataColumns | Rename the columns in the 'colData' slot, or do nothing if they don't match
renameColumns | Rename columns or do nothing if the names don't match
RGAModel | RandomGeneAssignmentModel Constructor
RGAModel-class | RGAModel Class Definition
RLSModel | RandomLabelShufflingModel Constructor
RLSModel-class | RLSModel Class Definition
runGSEA | Run Gene Set Enrichment Analysis
runGSEA-method | Run Gene Set Enrichment Analysis On A 'PCOSP' Model Object.

## -- S --

S4Model-class | An 'S4' Virtual Class For the Concept of a Statistical or ML Model
sampleClinicalModel | Sample ClinicalModel Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
sampleCohortList | A Set of Example Patient Cohorts
sampleICGCmicro | A Sample SurvivalExperiment Containing Data from the ICGC micro-array cohort from 'MetaGxPancreas'
samplePCOSPmodel | A Sample PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
samplePCOSPpredList | Sample CohortList with PCOSP Risk Predictions
samplePCSIsurvExp | Sample SurvivalExperiment Containing the PCSI rna-sequencing cohort from 'MetaGxPancreas'.
sampleRGAmodel | Sample RGA Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
sampleRLSmodel | Sample RLS Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
sampleTrainedPCOSPmodel | A Sample Trained PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
sampleValPCOSPmodel | Sample Validated PCOSP Model for Plotting Examples
show-method | Show method for Classes Inheriting from 'S4Model'
subset-method | Subset method for a 'CohortList'
SurvivalExperiment | Constructor for 'SurvivalExperiment' Class Builds a 'SurvivalExperiment' object, which is just a wrapper for a 'SummarizedExperiment' with mandatory survival metadata numeric columns 'survival_time' and 'event_occurred'.
SurvivalExperiment-class | SurvivalExperiment Class
SurvivalModel | Constructor for a SurvivalModel Object.
SurvivalModel-class | A Generic Container for Storing Mathematical Models of SurvivalExperiments

## -- T --

trainData | Generic for Accessing the Training Data of an 'S4' Object
trainData-method | Accessor for the Training Data in a 'S4Model' Object
trainData<- | Generic for Accessing the Training Data of an 'S4' Object
trainModel | Train a Model Based on the Data in an S4 Object
trainModel-method | Fit a GLM Using Clinical Predictors Specified in a 'ClinicalModel' Object.
trainModel-method | Train A ConsensusMetaclusteringModel
trainModel-method | Fit Models to the trainData in a CoxModel Object
trainModel-method | Train a GeneFuModel Object
trainModel-method | Train a NetworkCommunitySearchModel
trainModel-method | Train a PCOSP Model Based on The Data the assay 'trainMatrix'.
trainModel-method | Train a RGAModel Based on the Data in the assays slot.
trainModel-method | Train a PCOSP Model Based on The Data the assay 'trainMatrix'.

## -- V --

validateModel | Perform Validation on an 'S4' Object Representing a Trained Model
validateModel-method | Evaluate the Performance of a List of Trained KTSP Models from a PCOSP Model
validateModel-method | Validate a ClinicalModel object with a single SurvivalExperiment object.
validateModel-method | Compute the Inter-Cohort Cluster Correlation and Clustering Reproducibility of All Clusters in Each Cohort.
validateModel-method | Evaluate the Performance of a List of Trained KTSP Models from a PCOSP Model
validateModel-method | Validate a 'GenefuModel' object with a single 'SurvivalExperiment' object.
validateModel-method | Evaluate the Performance of a List of Trained KTSP Models from a PCOSP Model
validateModel-method | Validate a PCOSP model with a single SurvivalExperiment object.
validationData | Accessor for the 'validationData' slot of an 'S4' object
validationData-method | Accessor for the 'validationData' slot of an 'S4Model' object
validationData-method | Accessor for the 'validationData' slot of a 'SurvivalModel' object.
validationData<- | Generic for setting the 'validationData' slot on an 'S4' object
validationData<--method | Setter for the 'validationData' slot of a 'SurvivalModel' object with a 'CohortList'.
validationStats | Accessor for the 'validationStats' slot of an 'S4' object
validationStats-method | Acessor for the 'validationStats' slot of an 'S4Model' Object
validationStats-method | Accessor for the 'validationStats' slot of a 'SurvivalModel' object.
validationStats<- | Setter for the 'validationStats' slot on an 'S4' object
validationStats<--method | Setter for the 'validationStats' slot on an 'S4Model' object
validationStats<--method | Setter for the validationStats slot of a 'SurvivalModel' object with a 'data.frame'

## -- misc --

.ClinicalModel | ClinicalModel Class Definition
.CohortList | CohortList Class Definition
.ConsensusMetaclusteringModel | An 'S4Model' Containing Molecular Data to be Consensus Clustered
.GeneFuModel | A 'SurvivalModel' Sub-class Designed to Hold A Survival Model Generated Using the 'genefu' R package.
.ModelComparison | ModelComparison Class Definition
.NCSModel | S4Model Class for Metaclustering Using Network Community Search
.PCOSP | Pancreatic Cancer Overall Survival Predictor (PCOSP) Class
.RGAModel | RGAModel Class Definition
.RLSModel | RLSModel Class Definition
.S4Model | An 'S4' Virtual Class For the Concept of a Statistical or ML Model
.SurvivalExperiment | SurvivalExperiment Class
.SurvivalModel | A Generic Container for Storing Mathematical Models of SurvivalExperiments