• NAME
• SYNOPSIS
• DESCRIPTION
• HINTS
• COPYRIGHT
• AUTHORS
• METHODS
• new
• x
• y
• original_probeset
• orignal_probe_number
• original_probepair_number
• index

NAME

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

SYNOPSIS

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

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.

HINTS

You can only get probe-level information if you have parsed the CDF object with probe-level parsing turned on.

COPYRIGHT

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

Nick James (nick at arabidopsis.info)

David J Craigon (david at arabidopsis.info)

Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.

METHODS

new

  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

x 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

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

y 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 =cut sub y { my $self=shift;

    return $self->{"Y"};
}

# Probeset the probe came out of (name)

original_probeset 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 =cut

sub original_probeset { my $self=shift; return $self->{``PROBESET''}; }

# The number of the probe in the probeset

orignal_probe_number 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 =cut sub original_probe_number { my $self=shift; return $self->{``EXPOS''}; }

# Position of the mismatched base =head2 mismatch_position 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

=cut
sub mismatch_position {
    my $self=shift;

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

    return $self->{"POS"};
}

# The base at the mismatch position =head2 probe_mismatch_base 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 =cut sub probe_mismatch_base { my $self=shift;

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

    return $self->{"PBASE"};
}

# =head2 probe_target_base 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 =cut sub probe_target_base { my $self=shift;

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

    return $self->{"TBASE"};
}

# Is this probe a mismatch? =head2 is_mismatch 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 =cut sub is_mismatch { my $self=shift; return ($self->probe_target_base() eq $self->probe_mismatch_base()); }

original_probepair_number 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 =cut sub original_probepair_number { my $self=shift;

    return $self->{"ATOM"};
}

# Index for CEL file, apparently

index 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

=cut
sub index {
    my $self=shift;

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

1;