Bio::Matrix::PSM::SiteMatrixI(3)

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