Bio::Tree
Statistics
Summary
Bio::Tree::Statistics - Calculate certain statistics for a Tree
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Give standard usage here
Description
This object is a place to accumulate routines for calculating various
tree statistics from population genetic and phylogenetic methods.
Currently Fu and Li's D is implemented.
Tajima's D planned.
References forthcoming.
Methods
Methods description
Title : fu_and_li_D
Usage : my $D = $statistics->fu_an_li_D($tree,$nummut);
Function:
For this we assume that the tree is made up of
Bio::Tree::AlleleNode's which contain markers and alleles
each marker is a 'mutation'
Returns : Fu and Li's D statistic for this Tree
Args : $tree - Bio::Tree::TreeI which contains Bio::Tree::AlleleNodes |
Methods code
sub fu_and_li_D
{ my ($self,$tree) = @_;
my @nodes = $tree->get_nodes();
my $muttotal =0;
my $tipmutcount = 0;
my $sampsize = 0;
foreach my $n ( @nodes ) {
if ($n->is_Leaf() ) {
$sampsize++;
$tipmutcount += $n->get_marker_names();
}
$muttotal += $n->get_marker_names();
}
if( $muttotal <= 0 ) {
$self->warn("mutation total was not > 0, cannot calculate a Fu and Li D");
return 0;
}
my $a = 0;
for(my $k= 1; $k < $sampsize; $k++ ) {
$a += ( 1 / $k );
}
my $b = 0;
for(my $k= 1; $k < $sampsize; $k++ ) {
$b += ( 1 / $k**2 );
}
my $c = 2 * ( ( ( $sampsize * $a ) - (2 * ( $sampsize -1 ))) /
( ( $sampsize - 1) * ( $sampsize - 2 ) ) );
my $v = 1 + ( ( $a**2 / ( $b + $a**2 ) ) * ( $c - ( ( $sampsize + 1) /
( $sampsize - 1) ) ));
my $u = $a - 1 - $v;
my $D = ( $muttotal - ( $a * $tipmutcount) ) /
( sqrt ( ($u * $muttotal) + ( $v * $muttotal**2) ) );
return $D; } | General documentation
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = new Bio::Tree::Statistics();
Function: Builds a new Bio::Tree::Statistics object
Returns : Bio::Tree::Statistics
Args :