Package ubic.gemma.core.analysis.preprocess.batcheffects

Class BatchInfoPopulationHelperServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl

All Implemented Interfaces:

BatchInfoPopulationHelperService

@Service
public class BatchInfoPopulationHelperServiceImpl
extends Object
implements BatchInfoPopulationHelperService

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BATCH_FACTOR_NAME_PREFIX	Prefix to use when generating batch factor names.

Constructor Summary

Constructors

Constructor	Description
BatchInfoPopulationHelperServiceImpl()

Method Summary

Modifier and Type	Method	Description
ExperimentalFactor	createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

BATCH_FACTOR_NAME_PREFIX

public static final String BATCH_FACTOR_NAME_PREFIX

Prefix to use when generating batch factor names.

See Also:

• Constant Field Values

Constructor Details

BatchInfoPopulationHelperServiceImpl

public BatchInfoPopulationHelperServiceImpl()

Method Details

createRnaSeqBatchFactor

@Transactional
public ExperimentalFactor createRnaSeqBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial,String> headers)

Description copied from interface: BatchInfoPopulationHelperService

For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Specified by:

createRnaSeqBatchFactor in interface BatchInfoPopulationHelperService

Parameters:

ee - experiment

headers - map of biomaterial to a string. If there was no usable FASTQ header, we just use the GPL ID

Returns:

factor

createBatchFactor

@Transactional
public ExperimentalFactor createBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial,Date> dates)

Specified by:

createBatchFactor in interface BatchInfoPopulationHelperService