AMARETTO_EvaluateTestSet: AMARETTO_EvaluateTestSet

In broadinstitute/PerturbationAMARETTO: Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Description

Code to evaluate AMARETTO on a new gene expression test set. Uses output from AMARETTO_Run() and CreateRegulatorData().

Usage

AMARETTO_EvaluateTestSet(AMARETTOresults = AMARETTOresults,
  MA_Data_TestSet = MA_Data_TestSet,
  RegulatorData_TestSet = RegulatorData_TestSet)

Arguments

AMARETTOresults	AMARETTO output from AMARETTO_Run().
MA_Data_TestSet	Gene expression matrix from a test set (that was not used in AMARETTO_Run()).
RegulatorData_TestSet	Test regulator data from CreateRegulatorData().

Value

result

Examples

data('ProcessedDataLIHC')
AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedDataLIHC,
                                    NrModules = 2, VarPercentage = 50)

AMARETTOresults <- AMARETTO_Run(AMARETTOinit)
AMARETTOtestReport <- AMARETTO_EvaluateTestSet(AMARETTOresults = AMARETTOresults,
                                               MA_Data_TestSet = AMARETTOinit$MA_matrix_Var,
                                               RegulatorData_TestSet = AMARETTOinit$RegulatorData)

broadinstitute/PerturbationAMARETTO documentation built on Nov. 4, 2019, 8:14 a.m.