ubic.basecode.datafilter

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

java.lang.Object

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

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

All Implemented Interfaces:

Filter<M,R,C,V>

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

Filter a data matrix according to flags given in a separate matrix.

The flags can be 'A', 'P' or 'M', for absent, present and marginal, following the Affymetrix convention. By default, Marginal flags are counted as "absent", but this can be changed by the user.

Author:

Paul Pavlidis

Field Summary

Fields inherited from class ubic.basecode.datafilter.AbstractFilter

log

Constructor Summary

Constructors

Constructor and Description
RowAbsentFilter()

Method Summary

Modifier and Type	Method and Description
M	filter(M data) The data is going to be filtered in accordance to strings in 'flags'.
void	setFlagMatrix(StringMatrix<R,C> f)
void	setKeepMarginal(boolean k)
void	setMinPresentCount(int k)
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 Detail

RowAbsentFilter

public RowAbsentFilter()

Method Detail

filter

public M filter(M data)

The data is going to be filtered in accordance to strings in 'flags'. These are either 'A', 'P' or 'M' for absent, present and marginal.

Parameters:

data - The input matrix

Returns:

Matrix after filtering.

setFlagMatrix

public void setFlagMatrix(StringMatrix<R,C> f)

Parameters:

f - the matrix containing the flags.

setKeepMarginal

public void setKeepMarginal(boolean k)

Parameters:

k - whether to count 'marginal' as 'present'. Default is false.

setMinPresentCount

public void setMinPresentCount(int k)

Parameters:

k - the minimum number of present values there must be in order to keep the row.

setMinPresentFraction

public void setMinPresentFraction(double k)

Parameters:

k - the minimum fraction of present values that there must be, in order to keep the row.