Package ubic.basecode.datafilter

Class RowMissingFilter<M extends Matrix2D<R,C,V>,R,C,V>

java.lang.Object

ubic.basecode.datafilter.AbstractFilter<M,R,C,V>

ubic.basecode.datafilter.RowMissingFilter<M,R,C,V>

All Implemented Interfaces:

Filter<M,R,C,V>

public class RowMissingFilter<M extends Matrix2D<R,C,V>,R,C,V>
extends AbstractFilter<M,R,C,V>

Remove rows from a matrix that are missing too many points.

Author:

Paul Pavlidis

Field Summary

Fields inherited from class ubic.basecode.datafilter.AbstractFilter

log

Constructor Summary

Constructors

Constructor	Description
RowMissingFilter()

Method Summary

Modifier and Type	Method	Description
M	filter(M data)	Filter the data
void	setMaxFractionRemoved(double f)	Set the maximum fraction of rows which will be removed from the data set.
void	setMinPresentCount(int m)	Set the minimum number of values that must be present in each row.
void	setMinPresentFraction(double k)

Methods inherited from class ubic.basecode.datafilter.AbstractFilter

getOutputMatrix

Methods inherited from class java.lang.Object

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

Constructor Details

RowMissingFilter

public RowMissingFilter()

Method Details

filter

public M filter(M data)

Description copied from interface: Filter

Filter the data

Parameters:

data - a NamedMatrix. Some types of filters require that this be of a particular type of implementation of the Filter interface.

Returns:

The resulting filtered matrix

setMaxFractionRemoved

public void setMaxFractionRemoved(double f)

Set the maximum fraction of rows which will be removed from the data set. The default value is 0.3 Set it to 1.0 to remove this restriction.

Parameters:

f - double

setMinPresentCount

public void setMinPresentCount(int m)

Set the minimum number of values that must be present in each row. The default value is 5. This is always overridden by a hard-coded value (currently 2) that must be present for a row to be kept; but this value is in turn overridden by the maxfractionRemoved.

Parameters:

m - int

setMinPresentFraction

public void setMinPresentFraction(double k)

Parameters:

k - double the fraction of values to be removed.