RowAbsentFilter (baseCode 1.1.19 API)

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 Description

RowAbsentFilter()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.