Bio::PopGen::SimulatioUsereContributedBio::PopGen::Simulation::GeneticDrift(3)NAMEBio::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
perl v5.14.12011Bio::PopGen::Simulation::GeneticDrift(3)
