Bio::Community::Tools::Transformer - Arbitrary transformation of member counts
use Bio::Community::Tools::Transformer; # Hellinger-transform the counts of community members in a metacommunity my $transformer = Bio::Community::Tools::Transformer->new( -metacommunity => $meta, -type => 'hellinger', ); my $transformed_meta = $summarizer->get_transformed_meta;
This module takes a metacommunity and transform the count of the community members it contains. Several transformation methods are available: identity, binary, or hellinger.
Florent Angly firstname.lastname@example.org
User feedback is an integral part of the evolution of this and other Bioperl modules. Please direct usage questions or support issues to the mailing list, email@example.com, 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.
If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/
Copyright 2011,2012,2013 by the BioPerl Team firstname.lastname@example.org
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Function: Create a new Bio::Community::Tool::Transformer object Usage : my $transformer = Bio::Community::Tool::Transformer->new( ); Args : -metacommunity: see metacommunity() -type : see type() Returns : a new Bio::Community::Tools::Transformer object
Function: Get or set the metacommunity to normalize. Usage : my $meta = $transformer->metacommunity; Args : A Bio::Community::Meta object Returns : A Bio::Community::Meta object
Function: Get or set the type of transformation that is to be applied to member counts (not relative abundance): * identity : Keep the counts as-is * binary : Assign 1 if member is present, 0 if absent * relative : Set count of member equal to its relative abundance (%) * chisquare : Chi-square transformation * chord : Chord transformation * hellinger : Hellinger transformation Usage : my $type = $transformer->type; Args : identity, binary, relative, chisquare, chord, or hellinger Returns : identity, binary, relative, chisquare, chord, or hellinger
Function: Calculate and return a transformed metacommunity. Usage : my $meta = $transformer->get_transformed_meta; Args : none Returns : a new Bio::Community::Meta object