Package fr.ens.biologie.genomique.eoulsan.modules.diffana

Class Normalization

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization

Direct Known Subclasses:

DiffAna

public class Normalization
extends Object

This class create and launch an R script to compute normalisation of expression data

Since:

1.2

Author:

Vivien Deshaies

Field Summary

Fields

Modifier and Type	Field	Description
protected Design	design
protected RExecutor	executor
protected String	expressionFilesPrefix
protected String	expressionFilesSuffix
protected static String	NORMALIZATION_FUNCTIONS
protected RSConnection	rConnection
protected static String	TARGET_CREATION

Constructor Summary

Constructors

Constructor	Description
Normalization(RExecutor executor, Design design)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected void	checkRepTechGroupCoherence(List<String> rRepTechGroup, List<String> rCondNames)	Check if there is a problem in the repTechGroup coherence.
protected String	escapeUnderScore(String s)	Escape underscore for LaTeX title.
protected void	generateConditionPart(List<String> rCondNames, StringBuilder sb)	Add condition vector to R script.
protected void	generateExpressionFileNamesPart(StringBuilder sb)	Add expression file name vector to R script.
protected void	generateRepTechGroupPart(List<String> rRepTechGroup, StringBuilder sb)	Write the section of the script that handle technical replicate groups.
protected StringBuilder	generateRnwpreamble(List<Sample> experimentSamplesList, String title, String filePrefix)	Write Rnw preamble.
protected void	generateSampleIdsPart(List<Integer> rSampleIds, StringBuilder sb)	Add SampleIds vector to R script.
protected void	generateSampleNamePart(List<String> rSampleNames, StringBuilder sb)	Add sampleNames vector to R script.
protected String	generateScript(Experiment experiment, TaskContext context)	Generate the R script.
protected boolean	isTechnicalReplicates(List<String> rRepTechGroup)	Test if there is Technical replicates into rRepTechGroup field.
protected String	readStaticScript(String staticFile)	Read a static part of the generated script.
protected void	replaceRtgNA(List<String> rRepTechGroup, List<String> rSampleNames)	Replace na values in RepTechGroup list to avoid pooling error.
void	run(TaskContext context, Data data)	Run normalisation step
protected void	runRExecutor(TaskContext context, Data data)	Execute Rnw script.

Methods inherited from class java.lang.Object

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

Field Detail

TARGET_CREATION

protected static final String TARGET_CREATION

See Also:

Constant Field Values

NORMALIZATION_FUNCTIONS

protected static final String NORMALIZATION_FUNCTIONS

See Also:

Constant Field Values

design

protected final Design design

expressionFilesPrefix

protected final String expressionFilesPrefix

expressionFilesSuffix

protected final String expressionFilesSuffix

rConnection

protected RSConnection rConnection

executor

protected final RExecutor executor

Constructor Detail

Normalization

public Normalization(RExecutor executor,
                     Design design)
              throws EoulsanException

Public constructor.

Parameters:

executor - executor to use to execute the normalization

design - The design object

Throws:

EoulsanException - if an error occurs if connection to RServe server cannot be established

Method Detail

run

public void run(TaskContext context,
                Data data)
         throws EoulsanException

Run normalisation step

Throws:

EoulsanException - if the number of sample to analyze if lower than one

runRExecutor

protected void runRExecutor(TaskContext context,
                            Data data)
                     throws EoulsanException

Execute Rnw script.

Parameters:

context - Step context

data - data to process

Throws:

EoulsanException - if an error occurs while executing the script

isTechnicalReplicates

protected boolean isTechnicalReplicates(List<String> rRepTechGroup)

Test if there is Technical replicates into rRepTechGroup field.

Parameters:

rRepTechGroup - list of the technical replicate group

readStaticScript

protected String readStaticScript(String staticFile)
                           throws EoulsanException

Read a static part of the generated script.

Parameters:

staticFile - the name of a file containing a part of the script

Returns:

A String with the static part of the script

Throws:

EoulsanException - if an error occurs while reading the script

generateScript

protected String generateScript(Experiment experiment,
                                TaskContext context)
                         throws EoulsanException

Generate the R script.

Parameters:

experiment - the experiment

context - step context

Returns:

String rScript R script to execute

Throws:

EoulsanException - if an error occurs while generate the R script

generateRnwpreamble

protected StringBuilder generateRnwpreamble(List<Sample> experimentSamplesList,
                                            String title,
                                            String filePrefix)

Write Rnw preamble.

Parameters:

experimentSamplesList - sample experiment list

title - title of the document

filePrefix - Sweave file prefix

Returns:

a StringBuilder with Rnw preamble

generateSampleNamePart

protected void generateSampleNamePart(List<String> rSampleNames,
                                      StringBuilder sb)

Add sampleNames vector to R script.

Parameters:

rSampleNames - sample names

sb - StringBuilder where write the part of the script

generateSampleIdsPart

protected void generateSampleIdsPart(List<Integer> rSampleIds,
                                     StringBuilder sb)

Add SampleIds vector to R script.

Parameters:

rSampleIds - samples identifiers

sb - StringBuilder where write the part of the script

generateExpressionFileNamesPart

protected void generateExpressionFileNamesPart(StringBuilder sb)

Add expression file name vector to R script.

Parameters:

sb - StringBuilder where write the part of the script

generateRepTechGroupPart

protected void generateRepTechGroupPart(List<String> rRepTechGroup,
                                        StringBuilder sb)

Write the section of the script that handle technical replicate groups.

Parameters:

rRepTechGroup - list of technical replicate groups

sb - StringBuilder where write the part of the script

generateConditionPart

protected void generateConditionPart(List<String> rCondNames,
                                     StringBuilder sb)

Add condition vector to R script.

Parameters:

rCondNames - condition names

sb - StringBuilder where write the part of the script

checkRepTechGroupCoherence

protected void checkRepTechGroupCoherence(List<String> rRepTechGroup,
                                          List<String> rCondNames)
                                   throws EoulsanException

Check if there is a problem in the repTechGroup coherence.

Parameters:

rRepTechGroup - technical replicate group

rCondNames - condition names

Throws:

EoulsanException - if an error if found in the design file

escapeUnderScore

protected String escapeUnderScore(String s)

Escape underscore for LaTeX title.

Parameters:

s - string to escape

Returns:

s with escaped underscore

replaceRtgNA

protected void replaceRtgNA(List<String> rRepTechGroup,
                            List<String> rSampleNames)

Replace na values in RepTechGroup list to avoid pooling error.

Parameters:

rRepTechGroup - list of technical replicate groups

rSampleNames - sample names