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

Interface LinkAnalysisService

All Known Implementing Classes:

LinkAnalysisServiceImpl

public interface LinkAnalysisService

Author:

paul

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.

Method Details

process

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

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

Parameters:

ee - Experiment to be processed

filterConfig - Configuration for filtering of the input data.

linkAnalysisConfig - Configuration for the link analysis.

Returns:

analysis

processVectors

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

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.

Parameters:

t - taxon

dataVectors - data vectors

filterConfig - filter config

linkAnalysisConfig - - must include the array name.

Returns:

analysis

Throws:

FilteringException

SVDRelatedPreprocessingException