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lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN

  Returntype :	hashref
  Exceptions : 	none
  Caller     : 	general

=cut

sub algorithm_params {
    my $self=shift;

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

# Summary Statistics- returns hashref


=head2 summary_statistics

  Arg [1]    : 	hashref $summary_statistics (optional)
  Example    : 	my %summary_statistics=%{$chp->summary_statistics()};

# Print RawQ

print $chp->summary_statistics()->{"RawQ"};

  Description:	Get/set the summary statistics for turning the CEL
file into this CHP file. Returns a reference to a hash, keyed on
parameter name.

Parameters include:
RawQ
Noise
Background


  Returntype :	hashref
  Exceptions : 	none
  Caller     : 	general

=cut


sub summary_statistics {
    my $self=shift;

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

# Used in calculating background

=head2 smooth_factor

  Arg [1]    : 	float $smooth_factor (optional)
  Example    : 	my $smooth_factor=$chp->smooth_factor();
  Description:	Get/set the smooth factor. Your guess is as good as
mine as to what this actually is, although it is used in calculating
the background. Not available in MAS5 files.
  Returntype :	float
  Exceptions : 	none
  Caller     : 	general

=cut



sub smooth_factor {
    my $self=shift;

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

# An arrayref of zones

=head2 background_zones

  Arg [1]    : 	arrayref of arrayrefs $background_zones (optional)
  Example    : 	my @background_zones=@{$chp->background_zones()};

# Print "X", "Y", "Background Value" for background zone 0
print $background_zones[0]->[0],$background_zones[0]->[1],$background_zones[0]->[2];

  Description:	Get/set an array of background zones. Again, your guess is as good as
mine as to what this actually is, although it is used in calculating
the background. Not available in MAS5 files.

Returns an arrayref to an arrayref. Each zone has an array three
values long, which are X,Y and background value respectively.
  Returntype :	arrayref of arrayrefs
  Exceptions : 	none
  Caller     : 	general

=cut


sub background_zones {
    my $self=shift;

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

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

# The hash of results

=head2 probe_set_results

  Arg [1]    : 	hashref of hashrefs $probe_set_results (optional)
  Example    : 	my %results=%{$chp->probe_set_results()};
e
# Print "Signal", "Detection Call", "StatPairsUsed" for my favourite probe

print ($results{"246310_at"}->{"Signal"}."\n".$results{"246310_at"}->{"DetectionCall"}."\n".$results{"246310_at"}->{"StatPairsUsed"}."\n");

  Description:	Gain access to the actual data. Returns a reference to
hash, keyed on probe name. Each value contains another reference
to a hash with the following keys:

Signal
DetectionCall (detection call- one of P M A N)
DetectionPValue
StatPairs
StatPairsUsed
Probeset (a Bio::CDF::ProbeSet object, q.v.)

and optionally:
Change
ChangePValue
SignalLogRatio
SignalLogRatioHigh
SignalLogRatioLow
CommonPairs

when it is a CHP files with a comparison in it.


  Returntype :	hashref of hashrefs
  Exceptions : 	none
  Caller     : 	general

=cut