umcg.genetica.methylation

Class ParseTcgaMethylationFile

java.lang.Object

umcg.genetica.methylation.ParseTcgaMethylationFile

public class ParseTcgaMethylationFile
extends Object

Author:

Marc Jan and Lude

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ENCODING

Constructor Summary

Constructors

Constructor and Description
ParseTcgaMethylationFile()

Method Summary

Modifier and Type	Method and Description
static ArrayList<DoubleMatrixDataset<String,String>>	parseTCGAData_lvl1_all_matrices(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod) Read Level 1 data from TGCA Return 3 DoubleMatrixDatasets, methylated probe values, un-methylated probe values and beta values.
static DoubleMatrixDataset<String,String>	parseTCGAData_lvl1(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod) Read Level 1 data from TGCA a single DoubleMatrixDatasets containing beta values.
static DoubleMatrixDataset<String,String>	parseTCGAData_lvl3(String fileInputFolder, int nrProbes, boolean printToFile, String fileOut) Read level 3 data from TCGA Return DoubleMatrixDataset beta-values
static DoubleMatrixDataset<String,String>	parseTCGAData450As27K_lvl1(String fileInputFolder, boolean printToFile, String fileOutputFolder, boolean TcgaMethod, HashMap<String,Boolean> probeList) Read Level 1 450K data from TGCA a single DoubleMatrixDatasets containing beta values.

Methods inherited from class java.lang.Object

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

Field Detail

ENCODING

protected static final String ENCODING

See Also:

Constant Field Values

Constructor Detail

ParseTcgaMethylationFile

public ParseTcgaMethylationFile()

Method Detail

parseTCGAData_lvl1

public static DoubleMatrixDataset<String,String> parseTCGAData_lvl1(String fileInputFolder,
                                                                    boolean printToFile,
                                                                    String fileOutputFolder,
                                                                    boolean TcgaMethod)

Read Level 1 data from TGCA a single DoubleMatrixDatasets containing beta values. Beta values are calculated as : M/U+M (Non-bead studio / genome studio).

Parameters:

fileInputFolder -

printToFile -

fileOutputFolder -

TcgaMethod -

Returns:

all data out of the TCGA files Methylated / un-methylated and beta-values

parseTCGAData450As27K_lvl1

public static DoubleMatrixDataset<String,String> parseTCGAData450As27K_lvl1(String fileInputFolder,
                                                                            boolean printToFile,
                                                                            String fileOutputFolder,
                                                                            boolean TcgaMethod,
                                                                            HashMap<String,Boolean> probeList)

Read Level 1 450K data from TGCA a single DoubleMatrixDatasets containing beta values. Beta values are calculated as : M/U+M (Non-bead studio / genome studio).

Parameters:

fileInputFolder -

printToFile -

fileOutputFolder -

TcgaMethod -

Returns:

all data out of the TCGA files Methylated / un-methylated and beta-values

parseTCGAData_lvl1_all_matrices

public static ArrayList<DoubleMatrixDataset<String,String>> parseTCGAData_lvl1_all_matrices(String fileInputFolder,
                                                                                            boolean printToFile,
                                                                                            String fileOutputFolder,
                                                                                            boolean TcgaMethod)

Read Level 1 data from TGCA Return 3 DoubleMatrixDatasets, methylated probe values, un-methylated probe values and beta values. Beta values are calculated as : M/U+M (Non-bead studio / genome studio).

Parameters:

fileInputFolder -

printToFile -

fileOutputFolder -

TcgaMethod -

Returns:

all data out of the TCGA files Methylated / un-methylated and beta-values

parseTCGAData_lvl3

public static DoubleMatrixDataset<String,String> parseTCGAData_lvl3(String fileInputFolder,
                                                                    int nrProbes,
                                                                    boolean printToFile,
                                                                    String fileOut)

Read level 3 data from TCGA Return DoubleMatrixDataset beta-values

Parameters:

fileInputFolder -

nrProbes -

printToFile -

fileOut -

Returns: