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 modulestop
Carp
strict
warnings
Synopsistop
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");
Descriptiontop
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.
Methodstop
indexDescriptionCode
is_mismatchDescriptionCode
mismatch_positionDescriptionCode
newDescriptionCode
original_probe_numberNo descriptionCode
original_probepair_numberDescriptionCode
original_probesetDescriptionCode
probe_mismatch_baseDescriptionCode
probe_target_baseDescriptionCode
xDescriptionCode
yDescriptionCode

Methods description

indexcodetopprevnext
    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_mismatchcodetopprevnext
    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_positioncodetopprevnext
    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
newcodetopprevnext
  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_numbercodetopprevnext
    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_probesetcodetopprevnext
    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_basecodetopprevnext
    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_basecodetopprevnext
    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
xcodetopprevnext
    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
ycodetopprevnext
    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

indexdescriptiontopprevnext
sub index {
    my $self=shift;

    if (my $q=shift) {
	$self->{"INDEX"}=$q;
    }
    return $self->{"INDEX"};
}
is_mismatchdescriptiontopprevnext
sub is_mismatch {
    my $self=shift;
    return ($self->probe_target_base() eq $self->probe_mismatch_base());
}
mismatch_positiondescriptiontopprevnext
sub mismatch_position {
    my $self=shift;
    
    if (my $q=shift) {
	$self->{"POS"}=$q;
    }
    
    return $self->{"POS"};
}
newdescriptiontopprevnext
sub new {
    my $class=shift;
    my $q=shift;
    my $self={};

    bless $self,$class;


    return $self;
}
original_probe_numberdescriptiontopprevnext
sub original_probe_number {
    my $self=shift;
    return $self->{"EXPOS"};
}
original_probepair_numberdescriptiontopprevnext
sub original_probepair_number {
    my $self=shift;

    return $self->{"ATOM"};
}
original_probesetdescriptiontopprevnext
sub original_probeset {
    my $self=shift;
    return $self->{"PROBESET"};
}
probe_mismatch_basedescriptiontopprevnext
sub probe_mismatch_base {
    my $self=shift;
    
    if (my $q=shift) {
	$self->{"PBASE"}=$q;
    }
    
    return $self->{"PBASE"};
}
probe_target_basedescriptiontopprevnext
sub probe_target_base {
    my $self=shift;
    
    if (my $q=shift) {
	$self->{"TBASE"}=$q;
    }
    
    return $self->{"TBASE"};
}
xdescriptiontopprevnext
sub x {
    my $self=shift;
    return $self->{"X"};
}
ydescriptiontopprevnext
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