Seeder::Finder - Finder object
Version 0.01
This module provides the find_motifs method.
use Seeder::Finder; my $finder = Seeder::Finder->new( seed_width => "6", n_motif => "10", hd_index_file => "6.index", seq_file => "seq.fasta", bkgd_file => "seq.bkgd", out_file => "motif.out", strand => "forward", ); $finder -> find_motifs;
None by default
Title : new Usage : my $finder = Seeder::Finder->new(%args); Function: constructor for the Seeder::Finder object Returns : a new Seeder::Finder object Args : seed_width # Seed width motif_width # Motif width n_motif # Number of motifs hd_index_file # Index file seq_file # Sequence file bkgd_file # Background file out_file # Output file strand # Strand (forward or revcom), if the "revcom" option is selected, the forward strand and the reverse complement are included in the analysis
Title : find_motifs Usage : $finder -> find_motifs; Function: coordination of the motif finding process Args : none
Title : _read_seq Usage : $self->_read_seq; Function: read the sequence file, count number of sequences Returns : reference to sequence tables ( $self->{n_seq} ) Args : none
Title : _read_bkgd Usage : $self->_read_bkgd; Function: read the background Hamming distance file Returns : reference to a 2D array of background Hamming distances and reference to an array of nucleotide frequencies Args : none
Title : _oligo_count Usage : $self->_oligo_count; Function: count oligos in sequences Returns : reference to a 2D array of oligo counts Args : none
Title : _extent Usage : $self->_extent; Function: verify that motif extension width is even Returns : motif extension width Args : none
Title : _build_hd_matrix Usage : $self->_build_hd_matrix; Function: calculate Hamming distance between oligos and sequences Returns : reference to a 2D array of Hamming distances Args : none
Title : _pr_sum Usage : my $distribution = _pr_sum( $n_seq, \@freq ); Function: generate the probability distribution of a sum of i.i.d. random variables Returns : reference to an array of real numbers in the range from 0 to 1 Args : reference to oligo probability distribution, number of sequences
Title : _convolution Usage : my $p = _convolution($p, $f, $m); Function: convolution of two distributions Returns : reference to an array of real numbers in the range from 0 to 1 Args : reference to the distributions to be convoluted
Title : _iupac Usage : $self->_iupac; Function: set IUPAC degenerate symbol correspondence Returns : reference to a hash of IUPAC degenerate symbol Args : none
Title : _get_seed Usage : $self->_get_seed; Function: coordinate seed site selection Args : none
Title : _mtc Usage : @q_value = _mtc(@p_value); Function: generate a list of q-values from a list of p-values Returns : array of q-values Args : array of p-values Note : This is an adaptation of the algorithm described in Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies, Proc Natl Acad Sci U S A, 100, 9440-9445
Title : _frequency_matrix Usage : $self->_frequency_matrix; Function: convert a set of instances into a frequency matrix, frequencies for sequences holding multiple instances are weighted proportionally Returns : reference to a 2D array of nucleotide frequencies Args : none
Title : _probability_matrix Usage : $self->_probability_matrix; Function: convert a frequency matrix into a probability matrix Returns : reference to a 2D array of probabilities Args : none
Title : _weight_matrix Usage : $self->_weight_matrix; Function: convert a probability matrix into a weight matrix Returns : reference to a 2D array of position weights Args : none
Title : _select_site Usage : $self->_select_site; Function: select the best site among instances for each sequence given position weight matrix Returns : reference to a 2D array of sites Args : none
Title : _extend_motif Usage : $self->_extend_motif; Function: extend seeds to motif width Returns : reference to a 2D array of sites Args : none
Title : _information_content Usage : $self->_information_content; Function: calculate total information content Returns : total information content Args : none
Title : _mask_site Usage : $self->_mask_site; Function: mask the occurence in the sequence and in the count matrix Args : none
Title : _output_data Usage : $self->_output_data; Function: writes predicted motif to the output file Args : none
François Fauteux, <ffauteux at cpan.org>
<ffauteux at cpan.org>
Please report any bugs or feature requests to bug-motif at rt.cpan.org, or at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Seeder. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-motif at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Seeder
You can also look for information at:
RT: CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Seeder
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Seeder
CPAN Ratings
http://cpanratings.perl.org/d/Seeder
Search CPAN
http://search.cpan.org/dist/Seeder
This algorithm was developed by François Fauteux, Mathieu Blanchette and Martina Strömvik. We thank the Perl Monks <http://www.perlmonks.org/> for their support.
Copyright 2008 François Fauteux, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'François'. Assuming UTF-8
To install Seeder, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Seeder
CPAN shell
perl -MCPAN -e shell install Seeder
For more information on module installation, please visit the detailed CPAN module installation guide.