Package bacnet.scripts.database

Class ComparisonsCreation

java.lang.Object

bacnet.scripts.database.ComparisonsCreation

public class ComparisonsCreation
extends Object

Constructor Summary

Constructors

Constructor	Description
ComparisonsCreation()

Method Summary

Modifier and Type	Method	Description
static ExpressionMatrix	calc(Comparison comp)	Run the comparison by calculating statistical parameters given in tests ArrayList
static void	calcFilterAndSave(ArrayList<String> elements, String ID, String comparison, ArrayList<Filter> filters, boolean tiling, boolean geneExpression)	Calculate a comparison, filter the results, and save ExpressionMatrix and list of elements up-regulated and down-regulated
static ExpressionMatrix	calculateCompMatrix(ArrayList<String> comparisons, ArrayList<String> genomeElements, boolean tiling, boolean geneExpr)	Calculate a list of comparisons
static void	createAllCompMatrix(ArrayList<String> compList)	Go through all comparisons and create for each Tiling and GenExpression different matrices giving the number of genes, Srna and asRNA overexpressed and underexpressed
static void	createLogFCMatrix(Experiment exp, Genome genome)	Create Database.logFCMatrix by regrouping every logFC values for genes, sRNAs, asRNAs, and cisRegs in every BioCondition given Experiment
static void	createStatMatrix(Experiment exp, Genome genome)	Create Database.statTable by calculating stat values for genes, sRNAs, and asRNAs in every BioCondition For genes we use FDRBY calculated from GebneExpression array For sRNAs and asRNAs we use TSTUDENTTILING for Tiling array
static ExpressionMatrix	reorganizeMatrix(ExpressionMatrix compMatrix, ArrayList<StatTest> tests, Comparison comp)	Reorder headers of the comparison Matrix to group GenExpression and Tiling results coming from the same comparison
static void	setAllComparisonStreamData(ArrayList<String> allComp)	For each Comparison calculates corresponding TranscriptomeData, and save it
static void	summarizeDiffExpr(Experiment exp, Genome genome)	Create an array : Column = comparison Row = Gene, Srna or Asrna Cell = "+" if a specific gene has been detected over-expressed, and "-" if under-expressed Save it in : Comparison.PATH_DIFF_LISTS+".txt"
static void	summarizeDiffLists(Experiment exp)	Create an array : Row = comparison Column = Number of gene, Srna Asrna over or under-expressed Save it in : Comparison.PATH_DIFF_LISTS+".txt"

Methods inherited from class java.lang.Object

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

Constructor Details

ComparisonsCreation

public ComparisonsCreation()

Method Details

createAllCompMatrix

public static void createAllCompMatrix(ArrayList<String> compList)

Go through all comparisons and create for each Tiling and GenExpression different matrices giving the number of genes, Srna and asRNA overexpressed and underexpressed

Parameters:

compList -

calcFilterAndSave

public static void calcFilterAndSave(ArrayList<String> elements,
 String ID,
 String comparison,
 ArrayList<Filter> filters,
 boolean tiling,
 boolean geneExpression)

Calculate a comparison, filter the results, and save ExpressionMatrix and list of elements up-regulated and down-regulated

Parameters:

elements -

ID -

comparison -

filter -

geneExpression -

calculateCompMatrix

public static ExpressionMatrix calculateCompMatrix(ArrayList<String> comparisons,
 ArrayList<String> genomeElements,
 boolean tiling,
 boolean geneExpr)

Calculate a list of comparisons

Parameters:

comparisons -

genomeElements -

tiling -

geneExpr -

Returns:

reorganizeMatrix

public static ExpressionMatrix reorganizeMatrix(ExpressionMatrix compMatrix,
 ArrayList<StatTest> tests,
 Comparison comp)

Reorder headers of the comparison Matrix to group GenExpression and Tiling results coming from the same comparison

Parameters:

compMatrix -

tests -

comp -

Returns:

calc

public static ExpressionMatrix calc(Comparison comp)

Run the comparison by calculating statistical parameters given in tests ArrayList

Returns:

compMatrix containing the different statistical values

Throws:

Exception

setAllComparisonStreamData

public static void setAllComparisonStreamData(ArrayList<String> allComp)

For each Comparison calculates corresponding TranscriptomeData, and save it

Parameters:

allComp -

createLogFCMatrix

public static void createLogFCMatrix(Experiment exp,
 Genome genome)

Create Database.logFCMatrix by regrouping every logFC values for genes, sRNAs, asRNAs, and cisRegs in every BioCondition given Experiment

Parameters:

exp - list of BioCondition

genome - current genome with list of genes, sRNAs, asRNAs and cisRegs

createStatMatrix

public static void createStatMatrix(Experiment exp,
 Genome genome)

Create Database.statTable by calculating stat values for genes, sRNAs, and asRNAs in every BioCondition
For genes we use FDRBY calculated from GebneExpression array
For sRNAs and asRNAs we use TSTUDENTTILING for Tiling array

summarizeDiffExpr

public static void summarizeDiffExpr(Experiment exp,
 Genome genome)

Create an array :

Column = comparison

Row = Gene, Srna or Asrna

Cell = "+" if a specific gene has been detected over-expressed, and "-" if under-expressed

Save it in : Comparison.PATH_DIFF_LISTS+".txt"

summarizeDiffLists

public static void summarizeDiffLists(Experiment exp)

Create an array :

Row = comparison

Column = Number of gene, Srna Asrna over or under-expressed

Save it in : Comparison.PATH_DIFF_LISTS+".txt"