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lib/Bio/MaxQuant/Evidence/Statistics.pm  view on Meta::CPAN

    my ($o,%opts) = @_;
    # options : 
#    use Data::Dumper;
#    print STDERR 'OPTS: ', Dumper \%opts;
    my $data = $o->{data};
    my $result = {};
    foreach my $experiment(keys %$data){
        if(! exists $opts{experiment} || $experiment =~ /$opts{experiment}/){
            $result->{$experiment} = {};
            my $exptdata = $data->{$experiment};
            foreach my $pgid(keys %$exptdata){
                if(! exists $opts{proteinGroupId} || $pgid =~ /$opts{proteinGroupId}/){
                    my $pgdata = $exptdata->{$pgid};
                    if(! exists $opts{leadingProteins} || $pgdata->{'Leading Proteins'} =~ /$opts{leadingProteins}/){
                        if(! exists $opts{notLeadingProteins} || $pgdata->{'Leading Proteins'} !~ /$opts{notLeadingProteins}/){
                            $result->{$experiment}->{$pgid} = $pgdata;
                        }
                    }
                }
            }
        }
    }
#   print STDERR Dumper $result if $opts{experiment} eq qr/^LCC1.nE.r2$/;
    my $p = $o->new;
    %$p = %$o;
    $p->{data} = $result;

lib/Bio/MaxQuant/Evidence/Statistics.pm  view on Meta::CPAN

Logs data, if not already done, calculates median for each replicate, and subtracts median from each evidence in that replicate.

=cut

sub replicateMedianSubtractions {
    my ($o, %opts) = @_; # can set filter here
    $o->logRatios();
    foreach my $replicate($o->experiments()){
        my $median = $o->replicateMedian(%opts, experiment=>$replicate);
        my $p = $o->filter(experiment=>$replicate);
        foreach my $pgid(keys %{$p->{data}->{$replicate}}){
            foreach my $i(0.. $#{$p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}}){
                if($p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}->[$i] =~ /\d/){
                    $p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}->[$i] -= $median;
                }
            }
        }
    }
    # i guess we should do something better with generating this status:
    return 1;
}

=head2 median