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Man Pages


Manual Reference Pages  -  BIO::POPGEN::POPSTATS (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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 Wrights 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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perl v5.20.3 BIO::POPGEN::POPSTATS (3) 2016-04-05

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