Package ubic.gemma.core.analysis.service

Interface ExpressionAnalysisResultSetFileService

All Superinterfaces:

FileService<ExpressionAnalysisResultSet>, TsvFileService<ExpressionAnalysisResultSet>

All Known Implementing Classes:

ExpressionAnalysisResultSetFileServiceImpl

public interface ExpressionAnalysisResultSetFileService
extends TsvFileService<ExpressionAnalysisResultSet>

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
void	writeTsv(ExpressionAnalysisResultSet entity, Writer writer)	Write the analysis result set to an Appendable using a tabular format.
void	writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> result2Genes, Writer writer)	Write the analysis result set with result-to-gene mappings.

Methods inherited from interface ubic.gemma.core.analysis.service.FileService

write, write

Method Detail

writeTsv

void writeTsv(ExpressionAnalysisResultSet entity,
              Writer writer)
       throws IOException

Write the analysis result set to an Appendable using a tabular format.

The format is borrowed from ExpressionDataFileService and contains the following columns:

- result id - probe id - probe name - pvalue - corrected pvalue (a.k.a. qvalue) - rank Then for each contrast, a column with the contrast_ prefix: - coefficient - log2 fold-change - t statistic - pvalue

Specified by:

writeTsv in interface TsvFileService<ExpressionAnalysisResultSet>

Throws:

IOException

writeTsv

void writeTsv(ExpressionAnalysisResultSet analysisResultSet,
              @Nullable
              Baseline baseline,
              Map<Long,List<Gene>> result2Genes,
              Writer writer)
       throws IOException

Write the analysis result set with result-to-gene mappings.

The tabular format has the following additional columns: - gene id - gene name - gene NCBI ID - gene official symbol - gene official name

Parameters:

baseline - baseline to include in the TSV header

result2Genes - mapping of results to genes

Throws:

IOException