Florent Angly
and 1 contributors

NAME

Bio::Community::Tools::Transformer - Arbitrary transformation of member counts

SYNOPSIS

  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;

DESCRIPTION

This module takes a metacommunity and transform the count of the community members it contains. Several transformation methods are available: identity, binary, or hellinger.

AUTHOR

Florent Angly florent.angly@gmail.com

SUPPORT AND BUGS

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, 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.

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

Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

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.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 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

metacommunity

 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

type

 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

get_transformed_meta

 Function: Calculate and return a transformed metacommunity.
 Usage   : my $meta = $transformer->get_transformed_meta;
 Args    : none
 Returns : a new Bio::Community::Meta object