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lib/Bio/DB/BigBed.pm  view on Meta::CPAN

  sumData        Sum of the intervals in the bin

  sumSquares     Sum of the squares of the intervals in the bin

In addition, the bin objects add the following convenience methods:

 $bin->count()    Same as $bin->score->{validCount}
 $bin->minVal()   Same as $bin->score->{minVal}
 $bin->maxVal()   Same as $bin->score->{maxVal}
 $bin->mean()     The mean of values in the bin (from the formula above)
 $bin->variance() The variance of values in the bin (ditto)
 $bin->stdev()    The standard deviation of values in the bin (ditto)

From these values one can determine the mean, variance and standard
deviation across one or more genomic intervals. The formulas are as
follows:

 sub mean {
    my ($sumData,$validCount) = @_;
    return $sumData/$validCount;
 }

 sub variance {
    my ($sumData,$sumSquares,$validCount) = @_;
    my $var = $sumSquares - $sumData*$sumData/$validCount;

lib/Bio/DB/BigWig.pm  view on Meta::CPAN

  maxVal         Maximum value in the bin

  minVal         Minimum value in the bin

  sumData        Sum of the intervals in the bin

  sumSquares     Sum of the squares of the intervals in the bin

From these values one can determine the mean, variance and standard
deviation across one or more genomic intervals. The formulas are as
follows:

 sub mean {
    my ($sumData,$validCount) = @_;
    return $sumData/$validCount;
 }

 sub variance {
    my ($sumData,$sumSquares,$validCount) = @_;
    my $var = $sumSquares - $sumData*$sumData/$validCount;

lib/Bio/DB/BigWig.pm  view on Meta::CPAN

interval reported in the WIG file. Instead of returning a single
value, the score() method returns a hash of statistical summary
information containing the keys B<validCount>, B<maxVal>, B<minVal>,
B<sumData> and B<sumSquares> as described earlier.

In addition, the bin objects add the following convenience methods:

 $bin->count()    Same as $bin->score->{validCount}
 $bin->minVal()   Same as $bin->score->{minVal}
 $bin->maxVal()   Same as $bin->score->{maxVal}
 $bin->mean()     The mean of values in the bin (from the formula above)
 $bin->variance() The variance of values in the bin (ditto)
 $bin->stdev()    The standard deviation of values in the bin (ditto)

If no number is specified (i.e. you search for type "bin"), then an
interval of "1" is assumed. You will receive one bin spanning each
chromosome/contig.

I<summary>

This feature type is similar to "bin" except that instead of returning