Provided by: libbio-perl-perl_1.7.8-1_all 
NAME
Bio::Matrix::PSM::SiteMatrixI - SiteMatrixI implementation, holds a position scoring
matrix (or position weight matrix) and log-odds
SYNOPSIS
# You cannot use this module directly; see Bio::Matrix::PSM::SiteMatrix
# for an example implementation
DESCRIPTION
SiteMatrix is designed to provide some basic methods when working with position scoring
(weight) matrices, such as transcription factor binding sites for example. A DNA PSM
consists of four vectors with frequencies {A,C,G,T}. This is the minimum information you
should provide to construct a PSM object. The vectors can be provided as strings with
frequenciesx10 rounded to an int, going from {0..a} and 'a' represents the maximum (10).
This is like MEME's compressed representation of a matrix and it is quite useful when
working with relational DB. If arrays are provided as an input (references to arrays
actually) they can be any number, real or integer (frequency or count).
When creating the object you can ask the constructor to make a simple pseudo count
correction by adding a number (typically 1) to all positions (with the -correction
option). After adding the number the frequencies will be calculated. Only use correction
when you supply counts, not frequencies.
Throws an exception if: You mix as an input array and string (for example A matrix is
given as array, C - as string). The position vector is (0,0,0,0). One of the probability
vectors is shorter than the rest.
Summary of the methods I use most frequently (details below):
iupac - return IUPAC compliant consensus as a string
score - Returns the score as a real number
IC - information content. Returns a real number
id - identifier. Returns a string
accession - accession number. Returns a string
next_pos - return the sequence probably for each letter, IUPAC
symbol, IUPAC probability and simple sequence
consenus letter for this position. Rewind at the end. Returns a hash.
pos - current position get/set. Returns an integer.
regexp - construct a regular expression based on IUPAC consensus.
For example AGWV will be [Aa][Gg][AaTt][AaCcGg]
width - site width
get_string - gets the probability vector for a single base as a string.
get_array - gets the probability vector for a single base as an array.
get_logs_array - gets the log-odds vector for a single base as an array.
New methods, which might be of interest to anyone who wants to store PSM in a relational
database without creating an entry for each position is the ability to compress the PSM
vector into a string with losing usually less than 1% of the data. this can be done with:
my $str=$matrix->get_compressed_freq('A');
or
my $str=$matrix->get_compressed_logs('A');
Loading from a database should be done with new, but is not yest implemented. However you
can still uncompress such string with:
my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM
or
my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one of the Bioperl mailing lists. Your
participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Stefan Kirov
Email skirov@utk.edu
APPENDIX
calc_weight
Title : calc_weight
Usage : $self->calc_weight({A=>0.2562,C=>0.2438,G=>0.2432,T=>0.2568});
Function: Recalculates the PSM (or weights) based on the PFM (the frequency matrix)
and user supplied background model.
Throws : if no model is supplied
Example :
Returns :
Args : reference to a hash with background frequencies for A,C,G and T
next_pos
Title : next_pos
Usage : my %base=$site->next_pos;
Function:
Retrieves the next position features: frequencies and weights for
A,C,G,T, the main letter (as in consensus) and the
probabilty for this letter to occur at this position and
the current position
Throws :
Example :
Returns : hash (pA,pC,pG,pT,lA,lC,lG,lT,base,prob,rel)
Args : none
curpos
Title : curpos
Usage : my $pos=$site->curpos;
Function: Gets/sets the current position. Converts to 0 if argument is minus and
to width if greater than width
Throws :
Example :
Returns : integer
Args : integer
e_val
Title : e_val
Usage : my $score=$site->e_val;
Function: Gets/sets the e-value
Throws :
Example :
Returns : real number
Args : real number
consensus
Title : consensus
Usage :
Function: Returns the consensus
Returns : string
Args : (optional) threshold value 1 to 10, default 5
'5' means the returned characters had a 50% or higher presence at
their position
accession_number
Title : accession_number
Usage :
Function: accession number, this will be unique id for the SiteMatrix object as
well for any other object, inheriting from SiteMatrix
Throws :
Example :
Returns : string
Args : string
width
Title : width
Usage : my $width=$site->width;
Function: Returns the length of the site
Throws :
Example :
Returns : number
Args :
IUPAC
Title : IUPAC
Usage : my $iupac_consensus=$site->IUPAC;
Function: Returns IUPAC compliant consensus
Throws :
Example :
Returns : string
Args :
IC
Title : IC
Usage : my $ic=$site->IC;
Function: Information content
Throws :
Example :
Returns : real number
Args : none
get_string
Title : get_string
Usage : my $freq_A=$site->get_string('A');
Function: Returns given probability vector as a string. Useful if you want to
store things in a rel database, where arrays are not first choice
Throws : If the argument is outside {A,C,G,T}
Example :
Returns : string
Args : character {A,C,G,T}
id
Title : id
Usage : my $id=$site->id;
Function: Gets/sets the site id
Throws :
Example :
Returns : string
Args : string
regexp
Title : regexp
Usage : my $regexp=$site->regexp;
Function: Returns a regular expression which matches the IUPAC convention.
N will match X, N, - and .
Throws :
Example :
Returns : string
Args :
regexp_array
Title : regexp_array
Usage : my @regexp=$site->regexp;
Function: Returns a regular expression which matches the IUPAC convention.
N will match X, N, - and .
Throws :
Example :
Returns : array
Args :
To do : I have separated regexp and regexp_array, but
maybe they can be rewritten as one - just check what
should be returned
get_array
Title : get_array
Usage : my @freq_A=$site->get_array('A');
Function: Returns an array with frequencies for a specified base
Throws :
Example :
Returns : array
Args : char
_to_IUPAC
Title : _to_IUPAC
Usage :
Function: Converts a single position to IUPAC compliant symbol and
returns its probability. For rules see the implementation.
Throws :
Example :
Returns : char, real number
Args : real numbers for A,C,G,T (positional)
_to_cons
Title : _to_cons
Usage :
Function: Converts a single position to simple consensus character and
returns its probability. For rules see the implementation,
Throws :
Example :
Returns : char, real number
Args : real numbers for A,C,G,T (positional)
_calculate_consensus
Title : _calculate_consensus
Usage :
Function: Internal stuff
Throws :
Example :
Returns :
Args :
_compress_array
Title : _compress_array
Usage :
Function: Will compress an array of real signed numbers to a string (ie vector of bytes)
-127 to +127 for bi-directional(signed) and 0..255 for unsigned ;
Throws :
Example : Internal stuff
Returns : String
Args : array reference, followed by an max value and
direction (optional, default 1-unsigned),1 unsigned, any other is signed.
_uncompress_string
Title : _uncompress_string
Usage :
Function: Will uncompress a string (vector of bytes) to create an array of real
signed numbers (opposite to_compress_array)
Throws :
Example : Internal stuff
Returns : string, followed by an max value and
direction (optional, default 1-unsigned), 1 unsigned, any other is signed.
Args : array
get_compressed_freq
Title : get_compressed_freq
Usage :
Function: A method to provide a compressed frequency vector. It uses one byte to
code the frequence for one of the probability vectors for one position.
Useful for relational database. Improvement of the previous 0..a coding.
Throws :
Example : my $strA=$self->get_compressed_freq('A');
Returns : String
Args : char
get_compressed_logs
Title : get_compressed_logs
Usage :
Function: A method to provide a compressed log-odd vector. It uses one byte to
code the log value for one of the log-odds vectors for one position.
Throws :
Example : my $strA=$self->get_compressed_logs('A');
Returns : String
Args : char
sequence_match_weight
Title : sequence_match_weight
Usage :
Function: This method will calculate the score of a match, based on the PWM
if such is associated with the matrix object. Returns undef if no
PWM data is available.
Throws : if the length of the sequence is different from the matrix width
Example : my $score=$matrix->sequence_match_weight('ACGGATAG');
Returns : Floating point
Args : string
get_all_vectors
Title : get_all_vectors
Usage :
Function: returns all possible sequence vectors to satisfy the PFM under
a given threshold
Throws : If threshold outside of 0..1 (no sense to do that)
Example : my @vectors=$self->get_all_vectors(4);
Returns : Array of strings
Args : (optional) floating