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




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

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

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

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

         bioperl-lATbioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-lATbioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

         http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

CONTRIBUTORS
       Matthew Hahn, matthew.hahn-at-duke.edu

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

   new
        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)

   haploid_status
        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)

   Fst
        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.



perl v5.12.2                                                 February 24, 2011