Bio::PopGen::PopStats(User Contributed Perl DocumentatBio::PopGen::PopStats(3)NAMEBio::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:
http://bugzilla.open-bio.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 = 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 v5.14.1 2011-07-22 Bio::PopGen::PopStats(3)
