Florent Angly
and 1 contributors

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 2011-2014 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::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