Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::PopGen::PopStats(User Contributed Perl DocumentatBio::PopGen::PopStats(3)

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://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 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 v5.24.1			  2017-07-08	      Bio::PopGen::PopStats(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::PopGen::PopStats&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help