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

Interface BatchInfoPopulationService

All Known Implementing Classes:

BatchInfoPopulationServiceImpl

public interface BatchInfoPopulationService

Retrieve batch information from the data source, if possible, and populate it into experiments.

Author:

paul

Method Summary

Modifier and Type	Method	Description
void	fillBatchInformation(ExpressionExperiment ee, boolean force)	Attempt to obtain batch information from the data provider and populate it into the given experiment.
void	setFastqHeadersDir(Path fastqHeadersDir)	Set the path to use to resolve FASTQ headers.

Method Details

fillBatchInformation

void fillBatchInformation(ExpressionExperiment ee,
 boolean force)
                   throws BatchInfoPopulationException

Attempt to obtain batch information from the data provider and populate it into the given experiment. The method used may vary. For GEO, the default method is to download the raw data files, and look in them for a date. This is not implemented for every possible type of raw data file. For RNA-seq, we look for FASTQ headers under the configured FASTQ_HEADERS_ROOT.

Parameters:

ee - the experiment

force - whether to force recomputation

Throws:

BatchInfoPopulationException - describing the issue with populating batch information

setFastqHeadersDir

void setFastqHeadersDir(Path fastqHeadersDir)

Set the path to use to resolve FASTQ headers.

Exposed for testing, do not use in production code.