Probe documentation.

#### Bio::Affymetrix::CDF

### Probe

Summary | Package variables | Synopsis | Description | General documentation | Methods

Summary

    Bio::Affymetrix::CDF::Probe- an Affymetrix probe in a probeset in an CDF file

Package variables | top

No package variables defined.

Included modules | top

Carp
strict
warnings

Synopsis | top

    use Bio::Affymetrix::CDF;

    # Parse the CDF file

    my $cdf=new CDF();

    $cdf->parse_from_file("foo.cdf");

    # Find a probe. This is the first probe in the first probepair in Unit 1000

    my $probe=$chp->probesets()->{1000}->[0]->[0];

    # Find some fun facts about this probe

    print join ",",
    ($probe->x(),$probe->y(),($probe->is_mismatch()?"Mismatch probe":"Perfect match probe");

Description | top

    The Affymetrix microarray system produces files in a variety of
    formats. If this means nothing to you, these modules are probably not
    for you :). After these modules have parsed a CDF file, the resulting
    Bio::Affymetrix::CDF file contains a hash of
    Bio::Affmetrix::CDF::Probeset objects. Each probeset then contains an
     array reference of probepairs, each one which is an array reference
     of Bio::Affymetrix::CDF::Probe objects.
    You can only get probe-level information if you have parsed the CDF
    object with probe-level parsing turned on.

Methods | top

index | Description | Code
is_mismatch | Description | Code
mismatch_position | Description | Code
new | Description | Code
original_probe_number | No description | Code
original_probepair_number | Description | Code
original_probeset | Description | Code
probe_mismatch_base | Description | Code
probe_target_base | Description | Code
x | Description | Code
y | Description | Code

## Methods description

index | code | top | prev | next

        Arg [1]    :  integer $index (optional)
        Example    :  my $i=$probe->index();
     Description: 	Get/set the index of this probe. Allegedly this number
        was used in the CEL file at some point, but is probably useless now.
        Returntype : integer
        Exceptions : none
        Caller     : general

is_mismatch | code | top | prev | next

        Arg [0]    : none
        Example    : if ($probe->is_mismatch()) {
    print "Everybody loves mismatch probes!";
    }
      Description: 	Utility function that returns whether this probe is a
        mismatch probe or not.
        Returntype : bool
        Exceptions : none
        Caller     : general

mismatch_position | code | top | prev | next

        Arg [1]    :  integer $position (optional)
        Example    :  my $position=$probe->mismatch_position();
     Description: 	Get/set the postition of the mismatch base (in the
     25-mer oligo. As far as the author knows, all factory Affymetrix
    chips have the mismatch probe in position 13). Only available if the
        original CDF file was in MAS5 format.
        Returntype : integer
        Exceptions : none
        Caller     : general

new | code | top | prev | next

      Arg [0]    : none
      Example    : my $probe=new Bio::Affymetrix::CDF::Probe();
      Description: constructor for Bio::Affymetrix::CDF::Probe object. You
      probably do not want to make these objects yourself, however.
      Returntype : new Bio::Affmetrix::CDF object
      Exceptions : none
      Caller     : general

original_probepair_number | code | top | prev | next

        Arg [0]    : none
        Example    : my $original_number=$probe->original_probepair_number();
      Description: 	Returns the probe pair number as written in the file
        Returntype : integer $number
        Exceptions : none
        Caller     : general

original_probeset | code | top | prev | next

        Arg [0]    : none
        Example    : my $name=$probe->original_probeset()
      Description: 	The name of the original probeset this probe came from
        Returntype : string $probesetname
        Exceptions : none
        Caller     : general

probe_mismatch_base | code | top | prev | next

        Arg [1]    : char $base
        Example    : my $base=$probe->probe_mismatch_base()
      Description: 	Get/set the base A,C,T or G at the mismatch position.
        Returntype : char $base
        Exceptions : none
        Caller     : general

probe_target_base | code | top | prev | next

        Arg [1]    : char $base
        Example    : my $base=$probe->probe_target_base()
      Description: 	Get/set what the base (A, C, T or G) would be if it is to detect for
        the target sequence. Non-mismatch probes have
        probe_mismatch_base() eq probe_target_base().
        Returntype : char $base
        Exceptions : none
        Caller     : general

x | code | top | prev | next

        Arg [1]    :  integer $x (optional)
        Example    :  my $x=$probe->x();
     Description: 	Get the x coordinate of this probe. This is now (since version 0.3) immutable.
        Returntype : integer
        Exceptions : none
        Caller     : general

y | code | top | prev | next

        Arg [1]    : 	integer $y (optional)
        Example    : 	my $name=$probe->cols()
      Description: 	Get the y coordinate of this probe. This is now (since version 0.3) immutable.
        Returntype : integer
        Exceptions : none
        Caller     : general

## Methods code

index | description | top | prev | next

sub index {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"INDEX"}=$q;
        }
        return $self->{"INDEX"};

}

is_mismatch | description | top | prev | next

sub is_mismatch {

        my $self=shift;
        return ($self->probe_target_base() eq $self->probe_mismatch_base());

}

mismatch_position | description | top | prev | next

sub mismatch_position {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"POS"}=$q;
        }

        return $self->{"POS"};

}

new | description | top | prev | next

sub new {

        my $class=shift;
        my $q=shift;
        my $self={};

        bless $self,$class;

        return $self;

}

original_probe_number | description | top | prev | next

sub original_probe_number {

        my $self=shift;
        return $self->{"EXPOS"};

}

original_probepair_number | description | top | prev | next

sub original_probepair_number {

        my $self=shift;

        return $self->{"ATOM"};

}

original_probeset | description | top | prev | next

sub original_probeset {

        my $self=shift;
        return $self->{"PROBESET"};

}

probe_mismatch_base | description | top | prev | next

sub probe_mismatch_base {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"PBASE"}=$q;
        }

        return $self->{"PBASE"};

}

probe_target_base | description | top | prev | next

sub probe_target_base {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"TBASE"}=$q;
        }

        return $self->{"TBASE"};

}

x | description | top | prev | next

sub x {

        my $self=shift;
        return $self->{"X"};

}

y | description | top | prev | next

sub y {

        my $self=shift;

        return $self->{"Y"};

}

## General documentation

COPYRIGHT | top
    Copyright (C) 2005 by Nick James, David J Craigon, NASC (arabidopsis.info), The
    University of Nottingham

    This module is free software. You can copy or redistribute it under the same terms as Perl itself.

    Affymetrix is a registered trademark of Affymetrix Inc., Santa
    Clara, California, USA.
AUTHORS | top
    Nick James (nick at arabidopsis.info)

    David J Craigon (david at arabidopsis.info)

    Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.
orignal_probe_number | top
        Arg [0]    : none
        Example    : my $position=$probe->original_probe_number()
      Description: 	The name of the original index of this probe in the probeset
        Returntype : string $probesetname
        Exceptions : none
        Caller     : general