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 bellow):

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://redmine.open-bio.org/projects/bioperl/

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. Improvment 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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq