Package ubic.gemma.core.loader.expression

Interface DataUpdater

All Known Implementing Classes:

DataUpdaterImpl

public interface DataUpdater

Method Summary

Modifier and Type	Method	Description
void	addAffyDataFromAPTOutput(ExpressionExperiment ee, String pathToAptOutputFile)
void	addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay,SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)
void	addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
void	replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void	reprocessAffyDataFromCel(ExpressionExperiment ee)

Method Details

addAffyDataFromAPTOutput

void addAffyDataFromAPTOutput(ExpressionExperiment ee,
 String pathToAptOutputFile)
                       throws IOException

Throws:

IOException

addCountData

void addCountData(ExpressionExperiment ee,
 ArrayDesign targetArrayDesign,
 @Nullable
 DoubleMatrix<String,String> countMatrix,
 @Nullable
 DoubleMatrix<String,String> rpkmMatrix,
 Map<BioAssay,SequencingMetadata> sequencingMetadata,
 boolean allowMissingSamples)

log2cpmFromCounts

void log2cpmFromCounts(ExpressionExperiment ee,
 QuantitationType qt)

replaceData

void replaceData(ExpressionExperiment ee,
 ArrayDesign targetPlatform,
 QuantitationType qt,
 DoubleMatrix<String,String> data)

reprocessAffyDataFromCel

void reprocessAffyDataFromCel(ExpressionExperiment ee)

addData

void addData(ExpressionExperiment ee,
 ArrayDesign targetPlatform,
 ExpressionDataDoubleMatrix data)

replaceData

void replaceData(ExpressionExperiment ee,
 ArrayDesign targetPlatform,
 ExpressionDataDoubleMatrix data)