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_baseNo descriptionCode
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).
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_base(2)codetopprevnext
    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/set the y coordinate of this probe
Returntype : integer
Exceptions : none
Caller : general
ycodetopprevnext
    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

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