debian man page for bio::popgen::popstats

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

	 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.

perl v5.14.2							    2012-03-02						Bio::PopGen::PopStats(3pm)