bio::popgen::popstats(3pm) [debian man page]
Bio::PopGen::PopStats(3pm) User Contributed Perl Documentation Bio::PopGen::PopStats(3pm) NAME
Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations SYNOPSIS
use Bio::PopGen::PopStats; my $stats = Bio::PopGen::PopStats->new(); # add -haploid => 1 # to process haploid data DESCRIPTION
Calculate various population structure statistics, most notably Wright's Fst. 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 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::PopStats->new(); Function: Builds a new Bio::PopGen::PopStats object Returns : an instance of Bio::PopGen::PopStats Args : -haploid => 1 (if want to use haploid calculations) haploid_status Title : haploid_status Usage : $obj->haploid_status($newval) Function: Boolean value for whether or not to do haploid or diploid calculations, where appropriate Returns : Boolean Args : on set, new boolean value optional) Fst Title : Fst Usage : my $fst = $stats->Fst(@populations,@markernames) Function: Calculate Wright's Fst based on a set of sub-populations and specific markers Returns : Fst value (a value between 0 and 1) Args : Arrayref of populations to process Arrayref of marker names to process Note : Based on diploid method in Weir BS, Genetics Data Analysis II, 1996 page 178. perl v5.14.2 2012-03-02 Bio::PopGen::PopStats(3pm)
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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)