Christopher Fields > BioPerl-1.6.901 > Bio::PopGen::PopStats

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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:

  https://redmine.open-bio.org/projects/bioperl/

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.
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