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Bio::Matrix::PSM::SiteMatrixI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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