Bio::Affymetrix::CDF
Probe
| Bio::Affymetrix::CDF::Probe- an Affymetrix probe in a probeset in an CDF file
 | 
| No package variables defined. | 
| 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");
 
 | 
| The Affymetrix microarray system produces files in a variety offormats. 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 CDFobject with probe-level parsing turned on.
 
 | 
Methods description
    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
    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
    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).
    Returntype : integer
    Exceptions : none
    Caller     : general
  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
    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
    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
    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
    Arg [1]    :  integer $x (optional)
    Example    :  my $x=$probe->x();
 Description: 	Get/set the y coordinate of this probe
    Returntype : integer
    Exceptions : none
    Caller     : general
    Arg [1]    : 	integer $y (optional)
    Example    : 	my $name=$probe->cols()
  Description: 	Get/set the y coordinate of this probe
    Returntype : integer
    Exceptions : none
    Caller     : general
Methods code
sub index
 {    my $self=shift;
    if (my $q=shift) {
	$self->{"INDEX"}=$q;
    }
    return $self->{"INDEX"};}
sub is_mismatch
 {    my $self=shift;
    return !($self->probe_target_base() eq $self->probe_mismatch_base());}
sub mismatch_position
 {    my $self=shift;
    
    if (my $q=shift) {
	$self->{"POS"}=$q;
    }
    
    return $self->{"POS"};}
sub new
 {    my $class=shift;
    my $q=shift;
    my $self={};
    bless $self,$class;
    return $self;}
sub original_probe_number
 {    my $self=shift;
    return $self->{"EXPOS"};}
sub original_probepair_number
 {    my $self=shift;
    return $self->{"ATOM"};}
sub original_probeset
 {    my $self=shift;
    return $self->{"PROBESET"};}
sub probe_mismatch_base
 {    my $self=shift;
    
    if (my $q=shift) {
	$self->{"PBASE"}=$q;
    }
    
    return $self->{"PBASE"};}
sub probe_target_base
 {    my $self=shift;
    
    if (my $q=shift) {
	$self->{"TBASE"}=$q;
    }
    
    return $self->{"TBASE"};}
sub x
 {    my $self=shift;
    
    if (my $q=shift) {
	$self->{"X"}=$q;
    }
    
    return $self->{"X"};}
sub y
 {    my $self=shift;
    
    if (my $q=shift) {
	$self->{"Y"}=$q;
    }
    
    return $self->{"Y"};}
General documentation
| COPYRIGHT | top | 
| Copyright (C) 2005 by Nick James, David J Craigon, NASC (arabidopsis.info), TheUniversity 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]    : noneExample    : 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
 
 |