Package bacnet.scripts.database

Class TranscriptomesCreation

java.lang.Object

bacnet.scripts.database.TranscriptomesCreation

public class TranscriptomesCreation
extends Object

List of methods to add the different transcriptomic datasetsto your multi-omics website

Author:

UIBC

Constructor Summary

Constructors

Constructor	Description
TranscriptomesCreation()

Method Summary

Modifier and Type	Method	Description
static String	addTranscriptomeToDatabase(ArrayList<String> bioConds, String logs)	Convert all transcriptomics files - Convert all Seq data: RNASeq, RiboSeq, TSS, TermSeq - Convert all GeneExpression and Tiling - Convert all ExpressionMatrix
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 String	createLogfcTranscriptomeTable(ArrayList<String> bioConds, String logs, boolean varianceNorm)	Create LogFC summary matrix for transcriptomics datasets
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 ArrayList<GeneExpression>	getDataFromLab()	Get all GeneExpression from the lab
static void	varianceNormalization(Experiment exp)	Run some scripts to analyse the statistics of the transcriptomics data and performed VarianceNormalization: It will reduce the total variance of each data to 1 For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x)) So final variance of each column is equal to zero

Methods inherited from class java.lang.Object

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

Constructor Details

TranscriptomesCreation

public TranscriptomesCreation()

Method Details

addTranscriptomeToDatabase

public static String addTranscriptomeToDatabase(ArrayList<String> bioConds,
 String logs)

Convert all transcriptomics files

- Convert all Seq data: RNASeq, RiboSeq, TSS, TermSeq
- Convert all GeneExpression and Tiling
- Convert all ExpressionMatrix

Parameters:

bioConds -

logs -

Returns:

logs of the process

createLogfcTranscriptomeTable

public static String createLogfcTranscriptomeTable(ArrayList<String> bioConds,
 String logs,
 boolean varianceNorm)

Create LogFC summary matrix for transcriptomics datasets

Parameters:

bioConds -

logs -

varianceNorm - if variance normalization is needed

Returns:

the logs of the creation

varianceNormalization

public static void varianceNormalization(Experiment exp)

Run some scripts to analyse the statistics of the transcriptomics data and performed VarianceNormalization:
It will reduce the total variance of each data to 1
For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x))
So final variance of each column is equal to zero

Parameters:

exp -

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

Parameters:

exp -

genome -

getDataFromLab

public static ArrayList<GeneExpression> getDataFromLab()

Get all GeneExpression from the lab

Returns:

list of GeneExpression