Bio::Community::Tools::ShrapnelCleaner - Remove low-count, low-abundance community members
use Bio::Community::Tools::ShrapnelCleaner; # Remove singletons the communities in the given metacommunity my $cleaner = Bio::Community::Tools::ShrapnelCleaner->new( -metacommunity => $meta, ); $cleaner->clean;
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.
Florent Angly email@example.com
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, firstname.lastname@example.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 2011,2012,2013 by the BioPerl Team email@example.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.
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::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
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
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
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
Function: Remove singletons from the communities and return the updated metacommunity. Usage : my $meta = $cleaner->clean; Args : none Returns : arrayref of Bio::Community objects