Package bacnet.scripts.database

Class ProteomicsCreation

java.lang.Object

bacnet.scripts.database.ProteomicsCreation

public class ProteomicsCreation
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static String	DATA_TABLE

Constructor Summary

Constructors

Constructor	Description
ProteomicsCreation()

Method Summary

Modifier and Type	Method	Description
static void	addMissingValuesToMatrices(Experiment exp, Genome genome)	In order to represent proteomics data we need to add a -1 value in every missing row. ATTENTION: -1 is now a value when there is no value but it is detected
static void	addProteomesToDatabase(ArrayList<String> bioConds)	Clean proteomics tables, and convert them for the database
static void	convertProteomicsData(Experiment exp)	Convert all ExpressionMatrix found for Proteomic datasets and save them in Streaming folder
static void	createHTMLPageSummary()	DATA_TABLe has been created from a copy paste of ArrayExpress search results.
static void	createLogFCMatrix(Experiment exp, String genomeName)	Create a table will all protein expression for each Genome
static void	createMatrixFromTISData()	Create a matrix from TIS data for which each gene has its corresponding number of spectra
static String	createProteomeTable(ArrayList<String> bioConds, String logs)	Create Expression summary matrix for proteomics datasets
static void	summarizeProteomes(Experiment exp, String genomeName)	Create a table will all protein expression for each Genome

Methods inherited from class java.lang.Object

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

Field Details

DATA_TABLE

public static String DATA_TABLE

Constructor Details

ProteomicsCreation

public ProteomicsCreation()

Method Details

addProteomesToDatabase

public static void addProteomesToDatabase(ArrayList<String> bioConds)

Clean proteomics tables, and convert them for the database

Parameters:

bioConds -

convertProteomicsData

public static void convertProteomicsData(Experiment exp)

Convert all ExpressionMatrix found for Proteomic datasets and save them in Streaming folder

Parameters:

exp -

genome -

addMissingValuesToMatrices

public static void addMissingValuesToMatrices(Experiment exp,
 Genome genome)

In order to represent proteomics data we need to add a -1 value in every missing row.
ATTENTION: -1 is now a value when there is no value but it is detected

Parameters:

exp -

genome -

createProteomeTable

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

Create Expression summary matrix for proteomics datasets

Parameters:

bioConds -

logs -

Returns:

the logs of the creation

summarizeProteomes

public static void summarizeProteomes(Experiment exp,
 String genomeName)

Create a table will all protein expression for each Genome

Parameters:

exp -

genome -

createLogFCMatrix

public static void createLogFCMatrix(Experiment exp,
 String genomeName)

Create a table will all protein expression for each Genome

Parameters:

exp -

genome -

createHTMLPageSummary

public static void createHTMLPageSummary()

DATA_TABLe has been created from a copy paste of ArrayExpress search results. From the web^page we create the table, curated it and convert it to HTML Read DATA_TABLE and create an HTML table from it to ease accession to ArrayExpress info

createMatrixFromTISData

public static void createMatrixFromTISData()

Create a matrix from TIS data for which each gene has its corresponding number of spectra