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::IndividualI(3pm) User Contributed Perl Documentation Bio::PopGen::IndividualI(3pm) NAME
Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results SYNOPSIS
# Get a Bio::PopGen::IndividualI somehow # test if it has alleles/genotypes for a given marker if( $ind->has_marker($markername) ) { } # get the unique id print $ind->unique_id, " "; # get the number of results (genotypes) print $ind->num_results; DESCRIPTION
Describe the interface here 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 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ unique_id Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string num_genotypes Title : num_genotypes Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none annotation Title : annotation Usage : my $annotation_collection = $ind->annotation; Function: Get/set a Bio::AnnotationCollectionI for this individual Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object get_Genotypes Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters) has_Marker Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name get_marker_names Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none perl v5.14.2 2012-03-02 Bio::PopGen::IndividualI(3pm)