Florent Angly > Bio-Community-0.001000 > Bio::Community::Tools::ShrapnelCleaner

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Source   Latest Release: Bio-Community-0.001007

NAME ^

Bio::Community::Tools::ShrapnelCleaner - Remove low-count, low-abundance community members

SYNOPSIS ^

  use Bio::Community::Tools::ShrapnelCleaner;

  # Remove singletons the communities in the given metacommunity
  my $cleaner = Bio::Community::Tools::ShrapnelCleaner->new(
     -metacommunity => $meta,
  );
  $cleaner->clean;

DESCRIPTION ^

This module takes biological communities (contained in a metacommunity) and removes shrapnel, low abundance, low prevalence members that are likely to be the result of sequencing errors (when doing sequence-based analyses). By default, the cleaner removes only singletons, i.e. community members that appear in only one community (prevalence of 1) and have only 1 count. You can specify your own count and prevalence thresholds though.

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 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.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.

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::ShrapnelCleaner object
 Usage   : my $cleaner = Bio::Community::Tool::ShrapnelCleaner->new( );
 Args    : -metacommunity       : See metacommunity().
           -count_threshold     : See count_threshold().
           -prevalence_threshold: See prevalence_threshold().
 Returns : a new Bio::Community::Tools::ShrapnelCleaner object

metacommunity

 Function: Get or set the communities to process.
 Usage   : my $communities = $cleaner->communities;
 Args    : A Bio::Community::Meta object
 Returns : A Bio::Community::Meta object

count_threshold

 Function: Get or set the count threshold. Community members with a count equal
           or lower than this threshold are removed (provided they also meet the
           prevalence_threshold).
 Usage   : my $count_thresh = $cleaner->count_threshold;
 Args    : positive integer for the count
 Returns : positive integer for the count

prevalence_threshold

 Function: Get or set the prevalence threshold. Community members with a
           prevalence (number of communities that the member is found in) equal
           or lower than this threshold are removed (provided they also meet the
           count_threshold).
 Usage   : my $prevalence_thresh = $cleaner->prevalence_threshold;
 Args    : positive integer for the prevalence
 Returns : positive integer for the prevalence

clean

 Function: Remove singletons from the communities and return the updated
           metacommunity.
 Usage   : my $meta = $cleaner->clean;
 Args    : none
 Returns : arrayref of Bio::Community objects
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