Bio::PopGen::MarkerI(3pm) User Contributed Perl Documentation Bio::PopGen::MarkerI(3pm)NAME
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
SYNOPSIS
# Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker
my $name = $marker->name(); # marker name
my $description = $marker->description(); # description
my $type = $marker->type(); # coded type of the marker
my $unique_id = $marker->unique_id; # optional unique ID
my @alleles = $marker->get_Alleles(); # the known alleles
my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names
# vals are frequencies
# may change to handle multiple populations
DESCRIPTION
This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi.
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.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 _
name
Title : name
Usage : my $name = $marker->name();
Function: Get the name of the marker
Returns : string representing the name of the marker
Args :
description
Title : description
Usage : my $desc = $marker->description
Function: Get the marker description free text
Returns : string
Args : [optional] string
type
Title : type
Usage : my $type = $marker->type;
Function: Get coded string for marker type
Returns : string
Args : [optional] string
unique_id
Title : unique_id
Usage : my $id = $marker->unique_id;
Function: Get the unique marker ID
Returns : unique ID string
Args : [optional ] string
annotation
Title : annotation
Usage : $obj->annotation($seq_obj)
Function: retrieve the attached annotation object
Returns : Bio::AnnotationCollectionI or none;
See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. This method comes through extension from
Bio::AnnotatableI.
get_Alleles
Title : get_Alleles
Usage : my @alleles = $marker->get_Alleles();
Function: Get the available marker alleles if they are known and stored
Returns : Array of strings
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 (hash) where keys are the names of the alleles
Args : none
perl v5.14.2 2012-03-02 Bio::PopGen::MarkerI(3pm)
Check Out this Related Man Page
Bio::PopGen::Population(3pm) User Contributed Perl Documentation Bio::PopGen::Population(3pm)NAME
Bio::PopGen::Population - A population of individuals
SYNOPSIS
use Bio::PopGen::Population;
use Bio::PopGen::Individual;
my $population = Bio::PopGen::Population->new();
my $ind = Bio::PopGen::Individual->new(-unique_id => 'id');
$population->add_Individual($ind);
for my $ind ( $population->get_Individuals ) {
# iterate through the individuals
}
for my $name ( $population->get_marker_names ) {
my $marker = $population->get_Marker();
}
my $num_inds = $population->get_number_individuals;
my $homozygote_f = $population->get_Frequency_Homozygotes;
my $heterozygote_f = $population->get_Frequency_Heterozygotes;
# make a population haploid by making fake chromosomes through
# haplotypes -- ala allele 1 is on chrom 1 and allele 2 is on chrom 2
# the number of individuals created will thus be 2 x number in
# population
my $happop = $population->haploid_population;
DESCRIPTION
This is a collection of individuals. We'll have ways of generating Bio::PopGen::MarkerI objects out so we can calculate allele_frequencies
for implementing the various statistical tests.
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.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::Population->new();
Function: Builds a new Bio::PopGen::Population object
Returns : an instance of Bio::PopGen::Population
Args : -individuals => array ref of individuals (optional)
-name => population name (optional)
-source => a source tag (optional)
-description => a short description string of the population (optional)
name
Title : name
Usage : my $name = $pop->name
Function: Get the population name
Returns : string representing population name
Args : [optional] string representing population name
description
Title : description
Usage : my $description = $pop->description
Function: Get the population description
Returns : string representing population description
Args : [optional] string representing population description
source
Title : source
Usage : my $source = $pop->source
Function: Get the population source
Returns : string representing population source
Args : [optional] string representing population source
annotation
Title : annotation
Usage : my $annotation_collection = $pop->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this population
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
set_Allele_Frequency
Title : set_Allele_Frequency
Usage : $population->set_Allele_Frequency('marker' => { 'allele1' => 0.1});
Function: Sets an allele frequency for a Marker for this Population
This allows the Population to not have individual individual
genotypes but rather a set of overall allele frequencies
Returns : Count of the number of markers
Args : -name => (string) marker name
-allele => (string) allele name
-frequency => (double) allele frequency - must be between 0 and 1
OR
-frequencies => { 'marker1' => { 'allele1' => 0.01,
'allele2' => 0.99},
'marker2' => ...
}
add_Individual
Title : add_Individual
Usage : $population->add_Individual(@individuals);
Function: Add individuals to a population
Returns : count of the current number in the object
Args : Array of Individuals
remove_Individuals
Title : remove_Individuals
Usage : $population->remove_Individuals(@ids);
Function: Remove individual(s) to a population
Returns : count of the current number in the object
Args : Array of ids
get_Individuals
Title : get_Individuals
Usage : my @inds = $pop->get_Individuals();
Function: Return the individuals, alternatively restrict by a criteria
Returns : Array of Bio::PopGen::IndividualI objects
Args : none if want all the individuals OR,
-unique_id => To get an individual with a specific id
-marker => To only get individuals which have a genotype specific
for a specific marker name
get_Genotypes
Title : get_Genotypes
Usage : my @genotypes = $pop->get_Genotypes(-marker => $name)
Function: Get the genotypes for all the individuals for a specific
marker name
Returns : Array of Bio::PopGen::GenotypeI objects
Args : -marker => name of the marker
get_marker_names
Title : get_marker_names
Usage : my @names = $pop->get_marker_names;
Function: Get the names of the markers
Returns : Array of strings
Args : [optional] boolean flag to ignore internal cache status
get_Marker
Title : get_Marker
Usage : my $marker = $population->get_Marker($name)
Function: Get a Bio::PopGen::Marker object based on this population
Returns : Bio::PopGen::MarkerI object
Args : name of the marker
get_number_individuals
Title : get_number_individuals
Usage : my $count = $pop->get_number_individuals;
Function: Get the count of the number of individuals
Returns : integer >= 0
Args : none
set_number_individuals
Title : set_number_individuals
Usage : $pop->set_number_individuals($num);
Function: Fixes the number of individuals, call this with
0 to unset.
Only use this if you know what you are doing,
this is only relavent when you are just adding
allele frequency data for a population and want to
calculate something like theta
Returns : none
Args : individual count, calling it with undef or 0
will reset the value to return a number
calculated from the number of individuals
stored for this population.
get_Frequency_Homozygotes
Title : get_Frequency_Homozygotes
Usage : my $freq = $pop->get_Frequency_Homozygotes;
Function: Calculate the frequency of homozygotes in the population
Returns : fraction between 0 and 1
Args : $markername
get_Frequency_Heterozygotes
Title : get_Frequency_Heterozygotes
Usage : my $freq = $pop->get_Frequency_Homozygotes;
Function: Calculate the frequency of homozygotes in the population
Returns : fraction between 0 and 1
Args : $markername
haploid_population
Title : haploid_population
Usage : my $pop = $population->haploid_population;
Function: Make a new population where all the individuals
are haploid - effectively an individual out of each
chromosome an individual has.
Returns : L<Bio::PopGen::PopulationI>
Args : None
perl v5.14.2 2012-03-02 Bio::PopGen::Population(3pm)