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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 = new Bio::PopGen::PopStats(); # 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/MailList.shtml  - About the mailing lists

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.bioperl.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 = new Bio::PopGen::PopStats();
 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 Weir BS, Genetics Data Analysis II, 199?