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Bio::PopGen::PopStats(3pm) User Contributed Perl Documentation Bio::PopGen::PopStats(3pm)


Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations


  use Bio::PopGen::PopStats;
  my $stats = Bio::PopGen::PopStats->new(); # add -haploid => 1 
                                           # to process haploid data


Calculate various population structure statistics, most notably Wright's Fst.


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AUTHOR - Jason Stajich



Matthew Hahn,


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = Bio::PopGen::PopStats->new();
 Function: Builds a new Bio::PopGen::PopStats object 
 Returns : an instance of Bio::PopGen::PopStats
 Args    : -haploid => 1 (if want to use haploid calculations)


 Title   : haploid_status
 Usage   : $obj->haploid_status($newval)
 Function: Boolean value for whether or not to do haploid 
           or diploid calculations, where appropriate
 Returns : Boolean
 Args    : on set, new boolean value optional)


 Title   : Fst
 Usage   : my $fst = $stats->Fst(\@populations,\@markernames)
 Function: Calculate Wright's Fst based on a set of sub-populations
           and specific markers
 Returns : Fst value (a value between 0 and 1)
 Args    : Arrayref of populations to process
           Arrayref of marker names to process
 Note    : Based on diploid method in Weir BS, Genetics Data Analysis II, 1996
           page 178.
2018-10-27 perl v5.26.2