Bio::PopGen::Simulation::GeneticDrift(3pm)		User Contributed Perl Documentation		Bio::PopGen::Simulation::GeneticDrift(3pm)

NAME

       Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation

SYNOPSIS

	 use Bio::PopGen::Simulation::GeneticDrift;
	 my $sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 40,
							     -alleles => {A => 0.2,
									  B => 0.8});
	 for(my $i =0 ;$i < 10; $i++ ) {
	   my %f = $sim->next_generation; # get the freqs for each generation
	 }

	 for(my $i =0 ;$i < 10; $i++ ) {
	   # get the allele freqs as part of a Bio::PopGen::Population object
	   my $pop = $sim->next_generation('population');
	 }

DESCRIPTION

       A very simple 1 locus multi-allele random drift module, start with an initial set of allele frequency and simulate what happens over time.

       This isn't really useful for anything in particular yet but will be built upon.

       See Gillespie JH.(1998) "Population Genetics: a Concise guide." The Johns
		     Hopkins University Press, Baltimore, USA.	pp.19-47.

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
       email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

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::Simulation::GeneticDrift->new();
	Function: Builds a new Bio::PopGen::Simulation::GeneticDrift object
	Returns : an instance of Bio::PopGen::Simulation::GeneticDrift
	Args	: -popsize => starting N
		  -haploid => boolean if we should simulate haploids
		  -alleles => arrayref of the allele names
		  OR
		  -population => L<Bio::PopGen::PopulationI> object to initialize
				 from some previously defined Population object
				 (or result from a previous simulation)

   next_generation
	Title	: next_generation
	Usage	: my %generation = $sim->next_generation
	Function: Get the next generation of allele frequencies based on the current
		  generation
	Returns : Hash of allele frequencies
	Args	: 'allelefreqs' or 'population' to get back a hash of allele
			frequencies (default) OR a L<Bio::PopGen::Population> object

   population_size
	Title	: population_size
	Usage	: $obj->population_size($newval)
	Function:
	Example :
	Returns : value of population_size (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   set_Frequencies_Equivalent
	Title	: set_Frequencies_Equivalent
	Usage	: $sim->set_Frequencies_Equivalent
	Function: Reset the allele frequencies so they are all even
	Returns : none
	Args	: none

   get_Allele_Frequencies
	Title	: get_Allele_Frequencies
	Usage	: my %allele_freqs = $marker->get_Allele_Frequencies;
	Function: Get the alleles and their frequency (set relative to
		  a given population - you may want to create different
		  markers with the same name for different populations
		  with this current implementation
	Returns : Associative array where keys are the names of the alleles
	Args	: none

   add_Allele_Frequency
	Title	: add_Allele_Frequency
	Usage	: $marker->add_Allele_Frequency($allele,$freq)
	Function: Adds an allele frequency
	Returns : None
	Args	: $allele - allele name
		  $freq   - frequency value

   reset_alleles
	Title	: reset_alleles
	Usage	: $marker->reset_alleles();
	Function: Reset the alleles for a marker
	Returns : None
	Args	: None

   validate_Frequencies
	Title	: validate_Frequencies
	Usage	: if( $sim->validate_Frequencies) {}
	Function: Sanity checker that allele frequencies sum to 1 or less
	Returns : boolean
	Args	: -strict => 1 boolean if you want to insure that sum of freqs is 1

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