BatchInfoPopulationHelperServiceImpl (Gemma 1.32.0 API)

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 String BATCH_FACTOR_NAME_PREFIX
Prefix to use when generating batch factor names.

Constructor Summary

Constructors
Constructor Description

BatchInfoPopulationHelperServiceImpl()

Method Summary

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 Detail
  - BatchInfoPopulationHelperServiceImpl
```
public BatchInfoPopulationHelperServiceImpl()
```
- Method Detail
  - 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