AMARETTO_EvaluateTestSet: AMARETTO_EvaluateTestSet

Description Usage Arguments Value Examples

View source: R/amaretto_functions.R

Description

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

Usage

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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

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data('ProcessedDataLIHC')
## Not run: 
AMARETTOinit <- AMARETTO_Initialize(MA_matrix = ProcessedDataLIHC$MA_matrix,
                                    CNV_matrix = ProcessedDataLIHC$CNV_matrix,
                                    MET_matrix = ProcessedDataLIHC$MET_matrix,
                                    NrModules = 20, VarPercentage = 60)

AMARETTOresults <- AMARETTO_Run(AMARETTOinit)

## End(Not run)
load(system.file('extdata','AMARETTOinit.rda',package = 'AMARETTO'))
load(system.file('extdata','AMARETTOresults.rda',package = 'AMARETTO'))
AMARETTOtestReport <- AMARETTO_EvaluateTestSet(AMARETTOresults = AMARETTOresults,
                                               MA_Data_TestSet = AMARETTOinit$MA_matrix_Var,
                                               RegulatorData_TestSet = AMARETTOinit$RegulatorData)

gevaertlab/AMARETTO documentation built on Feb. 19, 2019, 4:15 a.m.