Bio::Matrix::PSM::ProtMatrix(3pm)			User Contributed Perl Documentation			 Bio::Matrix::PSM::ProtMatrix(3pm)

NAME

       Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds
       scoring information.

SYNOPSIS

	  use Bio::Matrix::PSM::ProtMatrix;
	  # Create from memory by supplying probability matrix hash both as strings or
	  # arrays where the frequencies   Hash entries of the form lN refer to an array
	  # of position-specific log-odds scores for amino acid N. Hash entries of the
	  # form pN represent the position-specific probability of finding amino acid N.

	  my %param = (
		    'id' => 'A. thaliana protein atp1',
		    '-e_val' => $score,
		    'lS' => [ '-2', '3', '-3', '2', '-3', '1', '1', '3' ],
		    'lF' => [ '-1', '-4', '0', '-5', '0', '-5', '-4', '-4' ],
		    'lT' => [ '-1', '1', '0', '1', '-2', '-1', '0', '1' ],
		    'lN' => [ '-3', '-1', '-2', '3', '-5', '5', '-2', '0' ],
		    'lK' => [ '-2', '0', '-3', '2', '-3', '2', '-3', '-1' ],
		    'lY' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-4', '-4' ],
		    'lE' => [ '-3', '4', '-3', '2', '-4', '-2', '-3', '2' ],
		    'lV' => [ '0', '-2', '1', '-4', '1', '-4', '-1', '-3' ],
		    'lQ' => [ '-1', '0', '-2', '3', '-4', '1', '-3', '0' ],
		    'lM' => [ '8', '-3', '8', '-3', '1', '-3', '-3', '-3' ],
		    'lC' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-3', '-3' ],
		    'lL' => [ '1', '-3', '1', '-4', '3', '-4', '-2', '-4' ],
		    'lA' => [ '-2', '1', '-2', '0', '-2', '-2', '2', '2' ],
		    'lW' => [ '-2', '-4', '-3', '-5', '-4', '-5', '-5', '-5' ],
		    'lP' => [ '-3', '-2', '-4', '-3', '-1', '-3', '6', '-3' ],
		    'lH' => [ '-2', '-2', '-3', '-2', '-5', '-2', '-2', '-3' ],
		    'lD' => [ '-4', '-1', '-3', '1', '-3', '-1', '-3', '4' ],
		    'lR' => [ '-2', '-1', '-3', '0', '-4', '4', '-4', '-3' ],
		    'lI' => [ '0', '-3', '0', '-4', '6', '-4', '-2', '-2' ],
		    'lG' => [ '-4', '-2', '-4', '-2', '-5', '-3', '-1', '-2' ],
		    'pS' => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
		    'pF' => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
		    'pT' => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
		    'pN' => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
		    'pK' => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
		    'pY' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
		    'pE' => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
		    'pV' => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
		    'pQ' => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
		    'pM' => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
		    'pC' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
		    'pL' => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
		    'pA' => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
		    'pW' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
		    'pP' => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
		    'pH' => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
		    'pD' => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
		    'pR' => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
		    'pI' => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
		    'pG' => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
	  );

	  my $matrix = Bio::Matrix::PSM::ProtMatrix( %param );

	  my $site = Bio::Matrix::PSM::ProtMatrix->new(%param);
	  # Or get it from a file:
	  use Bio::Matrix::PSM::IO;
	  my $psmIO = Bio::Matrix::PSM::IO->new(-file => $file, -format => 'psi-blast');
	  while (my $psm = $psmIO->next_psm) {
	     #Now we have a Bio::Matrix::PSM::Psm object,
	     # see Bio::Matrix::PSM::PsmI for details
	     #This is a Bio::Matrix::PSM::ProtMatrix object now
	     my $matrix = $psm->matrix;
	  }

	  # Get a simple consensus, where alphabet is:
	  # {A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V,}
	  # choosing the highest probability or N if prob is too low
	  my $consensus = $site->consensus;

	  # Retrieving and using regular expressions:
	  my $regexp = $site->regexp;
	  my $count = grep($regexp,$seq);
	  my $count = ($seq=~ s/$regexp/$1/eg);
	  print "Motif $mid is present $count times in this sequence
";

DESCRIPTION

       ProtMatrix is designed to provide some basic methods when working with position scoring (weight) matrices related to protein sequences.	A
       protein PSM consists of 20 vectors with 20 frequencies (one per amino acid per position).  This is the minimum information you should
       provide to construct a PSM object.  The vectors can be provided as strings with frequencies where the frequency is {0..a} and a=1. This is
       the way MEME 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 the constructor will check for positions that equal 0.	If such is found it will increase the count for all
       positions by one and recalculate the frequency.	Potential bug - if you are using frequencies and one of the positions is 0 it will change
       significantly.  However, you should never have frequency that equals 0.

       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 yet 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 - James Thompson
       Email tex@biosysadmin.com

APPENDIX

   new
	Title	 : new
	Usage	 : my $site = Bio::Matrix::PSM::ProtMatrix->new(
		      %probs,
		      %logs,
		      -IC    => $ic,
		      -e_val => $score,
		      -id    => $mid
		      -model => \%model
		   );
	Function : Creates a new Bio::Matrix::PSM::ProtMatrix object from memory
	Throws	 : If inconsistent data for all vectors (all 20 amino acids) is
		      provided, if you mix input types (string vs array) or if a
		      position freq is 0.
	Example  :
	Returns  : Bio::Matrix::PSM::ProtMatrix object
	Args	 : Hash references to log-odds scores and probabilities for
		   position-specific scoring info, e-value (optional), information
		   content (optional), id (optional), model for background distribution
		   of proteins (optional).

   alphabet
	Title	 : Returns an array (or array reference if desired) to the alphabet
	Usage	 :
	Function : Returns an array (or array reference) containing all of the
		   allowable characters for this matrix.
	Throws	 :
	Example  :
	Returns  : Array or arrary reference.
	Args	 :

   _calculate_consensus
	Title	 : _calculate_consensus
	Usage	 :
	Function : Calculates the consensus sequence for this matrix.
	Throws	 :
	Example  :
	Returns  :
	Args	 :

   next_pos
	Title	 : next_pos
	Usage	 :
	Function : Retrives the next position features: frequencies for all 20 amino
		   acids, log-odds scores for all 20 amino acids at this position,
		   the main (consensus) letter at this position, the probability
		   for the consensus letter to occur at this position and the relative
		   current position as an integer.
	Throws	 :
	Example  :
	Returns  : hash (or hash reference) (pA,pR,pN,pD,...,logA,logR,logN,logD,aa,prob,rel)
		   - pN entries represent the probability for amino acid N
		   to be at this position
		   - logN entries represent the log-odds score for having amino acid
		   N at this position
		   - aa is the consensus amino acid
		   - prob is the probability for the consensus amino acid to be at this
		   position
		   - rel is the relative index of the current position (integer)
	Args	  : none

   curpos
	Title	 : curpos
	Usage	 :
	Function : Gets/sets the current position.
	Throws	 :
	Example  :
	Returns  : Current position (integer).
	Args	 : New position (integer).

   e_val
	Title	 : e_val
	Usage	 :
	Function : Gets/sets the e-value
	Throws	 :
	Example  :
	Returns  :
	Args	 : real number

   IC
	Title	 : IC
	Usage	 :
	Function : Position-specific information content.
	Throws	 :
	Example  :
	Returns  : Information content for current position.
	Args	 : Information content for current position.

   accession_number
	Title	 : accession_number
	Usage	 :
	Function: accession number, this will be unique id for the ProtMatrix object as
		   well for any other object, inheriting from ProtMatrix.
	Throws	 :
	Example  :
	Returns  : New accession number (string)
	Args	 : Accession number (string)

   consensus
	Title	 : consensus
	Usage	 :
	Function : Returns the consensus sequence for this PSM.
	Throws	 : if supplied with thresold outisde 5..10 range
	Example  :
	Returns  : string
	Args	 : (optional) threshold value 5 to 10 (corresponds to 50-100% at each position

   get_string
	Title	: get_string
	Usage	:
	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}

   width
	Title	 : width
	Usage	 :
	Function : Returns the length of the site
	Throws	 :
	Example  :
	Returns  : number
	Args	 :

   get_array
	Title	 : get_array
	Usage	 :
	Function : Returns an array with frequencies for a specified amino acid.
	Throws	 :
	Example  :
	Returns  : Array representing frequencies for specified amino acid.
	Args	 : Single amino acid (character).

   get_logs_array
	Title	 : get_logs_array
	Usage	 :
	Function : Returns an array with log_odds for a specified base
	Throws	 :
	Example  :
	Returns  : Array representing log-odds scores for specified amino acid.
	Args	 : Single amino acid (character).

   id
	Title	 : id
	Usage	 :
	Function : Gets/sets the site id
	Throws	 :
	Example  :
	Returns  : string
	Args	 : string

   regexp
	Title	 : regexp
	Usage	 :
	Function : Returns a case-insensitive regular expression which matches the
		   IUPAC convention.  X's in consensus sequence will match anything.
	Throws	 :
	Example  :
	Returns  : string
	Args	 : Threshold for calculating consensus sequence (number in range 0-100
		   representing a percentage). Threshold defaults to 20.

   regexp_array
	Title	 : regexp_array
	Usage	 :
	Function : Returns an array of position-specific regular expressions.
		    X's in consensus sequence will match anything.
	Throws	 :
	Example  :
	Returns  : Array of position-specific regular expressions.
	Args	 : Threshold for calculating consensus sequence (number in range 0-100
		   representing a percentage). Threshold defaults to 20.
	Notes	 : Simply calls regexp method in list context.

   _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 max value and direction (optional, defaults to 1),
		    direction of 1 is unsigned, anything else 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 max value and direction (optional, defaults to 1),
		     direction of 1 is unsigned, anything else 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

   sequence_match_weight
	Title	 : sequence_match_weight
	Usage	 :
	Function :   This method will calculate the score of a match, based on the PSM
		     if such is associated with the matrix object. Returns undef if no
		     PSM 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

   _to_IUPAC
	Title	: _to_IUPAC
	Usage	:
	Function: Converts a single position to IUPAC compliant symbol and returns its probability.
		   Currently returns the most likely amino acid/probability combination.
	Throws	:
	Example :
	Returns : char, real number representing an amino acid and a probability.
	Args	: real numbers for all 20 amino acids (ordered by alphabet contained
		   in $self->{_alphabet}, minimum probability threshold.

   _to_cons
	Title	: _to_cons
	Usage	:
	Function: Converts a single position to simple consensus character and returns
		   its probability. Currently just calls the _to_IUPAC subroutine.
	Throws	:
	Example :
	Returns : char, real number
	Args	: real numbers for A,C,G,T (positional)

   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

perl v5.14.2							    2012-03-02					 Bio::Matrix::PSM::ProtMatrix(3pm)