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>
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.
You can find documentation for this module with the perldoc command.
perldoc Seeder
You can also look for information at:
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.
