Pancreatic Ductal Adenocarcinoma Tool-Kit

Documentation for package ‘PDATK’ version 1.16.1

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-- 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

-- 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