| Bio::PopGen::Marker(3pm) | User Contributed Perl Documentation | Bio::PopGen::Marker(3pm) |
Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes
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
This object will not contain genotype information pertaining to an individual, but rather population level statistics and descriptive information about a marker.
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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.
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Email jason-at-bioperl.org
Matthew Hahn, matthew.hahn-at-duke.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::PopGen::Marker->new();
Function: Builds a new Bio::PopGen::Marker object
Returns : an instance of Bio::PopGen::Marker
Args : -name => [string] marker name
-description => [string] marker description
-type => [string] marker type
-unique_id => [string/int] unique id
-allele_freq => [hash ref] allele frequencies
Title : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args : [optional] name
Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string
Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string
Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string
Title : annotation Usage : my $annotation_collection = $marker->annotation; Function: Get/set a Bio::AnnotationCollectionI for this marker Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object
Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles Returns : Array of strings Args : none
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
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
Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None
Title : marker_coverage
Usage : $marker->marker_coverage();
Function: Get marker coverage, that is, the number of
individuals where the marker is present
excluding missing or ambiguous alleles
Returns : integer, representing marker coverage
Args :
| 2018-10-27 | perl v5.26.2 |