Package ubic.gemma.core.analysis.preprocess.filter

Class RowLevelFilter

java.lang.Object

ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter

public class RowLevelFilter
extends Object

Author:

pavlidis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	RowLevelFilter.Method

Constructor Summary

Constructors

Constructor	Description
RowLevelFilter()

Method Summary

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	filter(ExpressionDataDoubleMatrix data)
void	setHighCut(double h)	Set the high threshold for removal.
void	setLowCut(double lowCut)	Set the low threshold for removal.
void	setLowCut(double lowCut, boolean isFraction)
void	setMethod(RowLevelFilter.Method method)	Choose the method that will be used for filtering.
void	setRemoveAllNegative(boolean t)	Set the filter to remove all rows that have only negative values.
void	setTolerance(Double tolerance)	Set the value considered to be an insignificant difference between two numbers.
void	setUseAsFraction(boolean setting)	Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values.
void	setUseHighCutAsFraction(boolean setting)
void	setUseLowCutAsFraction(boolean setting)

Methods inherited from class java.lang.Object

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

Constructor Detail

RowLevelFilter

public RowLevelFilter()

Method Detail

filter

public ExpressionDataDoubleMatrix filter(ExpressionDataDoubleMatrix data)

setHighCut

public void setHighCut(double h)

Set the high threshold for removal. If not set, no filtering will occur.

Parameters:

h - the threshold

setLowCut

public void setLowCut(double lowCut)

Set the low threshold for removal.

Parameters:

lowCut - the threshold

setLowCut

public void setLowCut(double lowCut,
                      boolean isFraction)

setMethod

public void setMethod(RowLevelFilter.Method method)

Choose the method that will be used for filtering. Default is 'MAX'. Those rows with the lowest values are removed during 'low' filtering.

Parameters:

method - one of the filtering method constants.

setRemoveAllNegative

public void setRemoveAllNegative(boolean t)

Set the filter to remove all rows that have only negative values. This is applied BEFORE applying fraction-based criteria. In other words, if you request filtering 0.5 of the values, and 0.5 have all negative values, you will get 0.25 of the data back. Default = false.

Parameters:

t - boolean

setUseAsFraction

public void setUseAsFraction(boolean setting)

Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values. Otherwise the cuts are interpeted as actual values. Default = false.

Parameters:

setting - boolean

setUseHighCutAsFraction

public void setUseHighCutAsFraction(boolean setting)

setUseLowCutAsFraction

public void setUseLowCutAsFraction(boolean setting)

setTolerance

public void setTolerance(Double tolerance)

Set the value considered to be an insignificant difference between two numbers. Default is Constants.SMALL. Used by DISTINCTVALUE filter. Changed to ignore NAs in distinct value counting mode. All the other methods already did that.

Parameters:

tolerance - tolerance