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

Class BatchInfoParser

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser

public class BatchInfoParser
extends Object

Parse information on batch from raw data files. This will typically correspond to "scan date" for an array.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
BatchInfoParser()

Method Summary

Modifier and Type	Method	Description
static Map<String,BioAssay>	getAccessionToBioAssayMap(ExpressionExperiment ee)
Map<BioMaterial,Date>	getBatchInfo(ExpressionExperiment ee, Collection<File> files)
ScanDateExtractor	getScanDateExtractor()

Methods inherited from class java.lang.Object

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

Constructor Details

BatchInfoParser

public BatchInfoParser()

Method Details

getAccessionToBioAssayMap

public static Map<String,BioAssay> getAccessionToBioAssayMap(ExpressionExperiment ee)

Parameters:

ee - experiment

Returns:

bioassay accession (GSM...) to bioassay map

getBatchInfo

public Map<BioMaterial,Date> getBatchInfo(ExpressionExperiment ee,
 Collection<File> files)

getScanDateExtractor

public ScanDateExtractor getScanDateExtractor()

Returns:

the extractor used. The class of the value can tell you what type of file was detected, or if it was generic.