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Bio::PopGen::PopStats.3pm

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-l@bioperl.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-l@bioperl.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.