Package ubic.basecode.datafilter

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

java.lang.Object
ubic.basecode.datafilter.AbstractFilter<M,R,C,V>
ubic.basecode.datafilter.AffymetrixProbeNameFilter<M,R,C,V>
All Implemented Interfaces:
Filter<M,R,C,V>
public class AffymetrixProbeNameFilter<M extends Matrix2D<R,C,V>,R,C,V> extends AbstractFilter<M,R,C,V>
Remove probes that have names meeting certain rules indicating they may have low reliability. This is targeted at cases like "AFFX", "_st", "_f_at" and so forth.
Author:
Paul Pavlidis

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    AFFX
    Filter probes that have the AFFX prefix.
    static final int
    F
    Filter probes that have the "_f_at" (family) tag.
    static final int
    G
    Filter probes that have the "_g_at" (group) tag.
    static final int
    ST
    Filter probes that contain the '_st' (sense strand) tag
    static final int
    X
    Filter probes that have the "_x_at" tag.

    Fields inherited from class ubic.basecode.datafilter.AbstractFilter

    log

  • Constructor Summary

    Constructors
    Constructor
    Description
    AffymetrixProbeNameFilter()
    Filter probes with all criteria switched on.
    AffymetrixProbeNameFilter(int[] criteria)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    M
    filter(M data)
    Filter the data

    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

  • Field Details

    • AFFX

      public static final int AFFX
      Filter probes that have the AFFX prefix.
      See Also:

    • F

      public static final int F
      Filter probes that have the "_f_at" (family) tag.
      See Also:

    • G

      public static final int G
      Filter probes that have the "_g_at" (group) tag.
      See Also:

    • ST

      public static final int ST
      Filter probes that contain the '_st' (sense strand) tag
      See Also:

    • X

      public static final int X
      Filter probes that have the "_x_at" tag.
      See Also:

  • Constructor Details

    • AffymetrixProbeNameFilter

      public AffymetrixProbeNameFilter()
      Filter probes with all criteria switched on.

    • AffymetrixProbeNameFilter

      public AffymetrixProbeNameFilter(int[] criteria)
      Parameters:
      criteria - int[] of constants indicating the criteria to use.

  • 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