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.