umcg.genetica.methylation

Class CheckMatrixForValidBetaValues

java.lang.Object

umcg.genetica.methylation.CheckMatrixForValidBetaValues

public class CheckMatrixForValidBetaValues
extends Object

Author:

MarcJan

Constructor Summary

Constructors

Constructor and Description
CheckMatrixForValidBetaValues()

Method Summary

Modifier and Type	Method and Description
static void	checkBetaValues(DoubleMatrixDataset<String,String> dataset, boolean replaceCheckedValuesOutOfRange) Check if all probe values are actually between 0 and 1.
static ArrayList<String>	checkMinAndMaxPerSample(DoubleMatrixDataset<String,String> dataset, boolean replaceCheckedValuesOutOfRange) Check if all probe values are actually between 0 and 1.

Methods inherited from class java.lang.Object

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

Constructor Detail

CheckMatrixForValidBetaValues

public CheckMatrixForValidBetaValues()

Method Detail

checkBetaValues

public static void checkBetaValues(DoubleMatrixDataset<String,String> dataset,
                                   boolean replaceCheckedValuesOutOfRange)

Check if all probe values are actually between 0 and 1. Otherwise set to NA If not kick out sample

Parameters:

dataset -

replaceCheckedValuesOutOfRange -

checkMinAndMaxPerSample

public static ArrayList<String> checkMinAndMaxPerSample(DoubleMatrixDataset<String,String> dataset,
                                                        boolean replaceCheckedValuesOutOfRange)

Check if all probe values are actually between 0 and 1. If replaceCheckedValuesOutOfRange is true values that are known to be allowed are replaced. With 0 if between -0.1 and 0 (Due to background correction). With -999 if either 9 or -3.4E38. If not kick out sample

Parameters:

dataset -

replaceCheckedValuesOutOfRange -

Returns: