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, Integer readLength, Boolean isPairedReads, boolean allowMissingSamples)
ExpressionExperiment	addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
ExpressionExperiment	replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void	reprocessAffyDataFromCel(ExpressionExperiment ee)

Method Detail

addAffyDataFromAPTOutput

void addAffyDataFromAPTOutput(ExpressionExperiment ee,
                              String pathToAptOutputFile)
                       throws IOException

Throws:

IOException

addCountData

void addCountData(ExpressionExperiment ee,
                  ArrayDesign targetArrayDesign,
                  DoubleMatrix<String,String> countMatrix,
                  DoubleMatrix<String,String> rpkmMatrix,
                  @Nullable
                  Integer readLength,
                  @Nullable
                  Boolean isPairedReads,
                  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

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

replaceData

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