baseCode.dataFilter
Class RowAbsentFilter

java.lang.Object
  baseCode.dataFilter.AbstractFilter
      baseCode.dataFilter.RowAbsentFilter

All Implemented Interfaces:

Filter

public class RowAbsentFilter

extends AbstractFilter

implements Filter

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.

Copyright (c) 2004

Institution:: Columbia University

Version:

$Id: RowAbsentFilter.java,v 1.5 2004/07/27 03:18:58 pavlidis Exp $

Author:

Paul Pavlidis

Field Summary

Fields inherited from class baseCode.dataFilter.AbstractFilter

log

Constructor Summary

RowAbsentFilter()

Method Summary

NamedMatrix	filter(NamedMatrix data) The data is going to be filtered in accordance to strings in 'flags'.
void	setFlagMatrix(StringMatrix2DNamed f)
void	setKeepMarginal(boolean k)
void	setMinPresentCount(int k)
void	setMinPresentFraction(double k)

Methods inherited from class 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

setFlagMatrix

public void setFlagMatrix(StringMatrix2DNamed f)

Parameters:

f - the matrix containing the flags.

setMinPresentFraction

public void setMinPresentFraction(double k)

Parameters:

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

setMinPresentCount

public void setMinPresentCount(int k)

Parameters:

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

setKeepMarginal

public void setKeepMarginal(boolean k)

Parameters:

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

filter

public NamedMatrix filter(NamedMatrix 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.

Specified by:

filter in interface Filter

Parameters:

data - The input matrix

Returns:

Matrix after filtering.