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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:

   http://bugzilla.open-bio.org/
 
 

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