Package ubic.gemma.core.analysis.expression.coexpression.links

Class LinkAnalysisServiceImpl

java.lang.Object

ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceImpl

All Implemented Interfaces:

LinkAnalysisService

@Component
public class LinkAnalysisServiceImpl
extends Object
implements LinkAnalysisService

Running link analyses through the spring context; will persist the results if the configuration says so. See LinkAnalysisCli for more instructions.

Author:

Paul

Constructor Summary

Constructors

Constructor	Description
LinkAnalysisServiceImpl()

Method Summary

Modifier and Type	Method	Description
LinkAnalysis	process(ExpressionExperiment ee, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)	Run a link analysis on an experiment, and persist the results if the configuration says to.
LinkAnalysis	processVectors(Taxon t, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)	Used when the input is data vectors from another source, instead of from a DB-bound expressionExperiment.

Methods inherited from class java.lang.Object

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

Constructor Detail

LinkAnalysisServiceImpl

public LinkAnalysisServiceImpl()

Method Detail

process

public LinkAnalysis process(ExpressionExperiment ee,
                            FilterConfig filterConfig,
                            LinkAnalysisConfig linkAnalysisConfig)

Description copied from interface: LinkAnalysisService

Run a link analysis on an experiment, and persist the results if the configuration says to.

Specified by:

process in interface LinkAnalysisService

Parameters:

ee - Experiment to be processed

filterConfig - Configuration for filtering of the input data.

linkAnalysisConfig - Configuration for the link analysis.

Returns:

analysis

processVectors

public LinkAnalysis processVectors(Taxon t,
                                   Collection<ProcessedExpressionDataVector> dataVectors,
                                   FilterConfig filterConfig,
                                   LinkAnalysisConfig linkAnalysisConfig)
                            throws FilteringException,
                                   SVDRelatedPreprocessingException

Description copied from interface: LinkAnalysisService

Used when the input is data vectors from another source, instead of from a DB-bound expressionExperiment. Example would be vectors read from a file. Output is always 'text', and DB is not used. Intensity-level-based filtering is not available, so the data should be pre-filtered if you need that.

Specified by:

processVectors in interface LinkAnalysisService

Parameters:

t - taxon

dataVectors - data vectors

filterConfig - filter config

linkAnalysisConfig - - must include the array name.

Returns:

analysis

Throws:

FilteringException

SVDRelatedPreprocessingException