Bio::Matrix::PSM SiteMatrixI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::PSM::SiteMatrixI - SiteMatrix interface, holds a position
scoring matrix (or position weight matrix)
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::RootI
Synopsis
  use Bio::Matrix::PSM::SiteMatrix;

  # Create from memory by supplying probability matrix hash
  # both as strings or arrays

  my ($a,$c,$g,$t,$score,$ic, $mid)=@_;
  # where $a,$c,$g and $t are either arrayref or string
  # or
  my ($a,$c,$g,$t,$score,$ic,$mid)=
     ('05a011','110550','400001','100104',0.001,19.2,'CRE1');
  # Where a stands for all (this frequency=1), see explanation bellow

  my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,-IC=>$ic,
             -e_val=>$score, -id=>$mid);
  my $site=new Bio::Matrix::PSM::SiteMatrix(%param);

  # Or get it from a file:

  use Bio::Matrix::PSM::IO;
  my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'transfac');
  while (my $psm=$psmIO->next_psm) {
    # Now we have a Bio::Matrix::PSM::Psm object, see
    # Bio::Matrix::PSM::PsmI for details
    my $matrix=$psm->matrix;
    # This is a Bio::Matrix::PSM::SiteMatrix object now
  }

  # Get a simple consensus, where alphabet is {A,C,G,T,N}, choosing
  # the highest probability or N if prob is too low

  my $consensus=$site->consensus;

  #Getting/using regular expression
  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\n";
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 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.
Methods
newDescriptionCode
next_posDescriptionCode
curposDescriptionCode
e_valDescriptionCode
consensusDescriptionCode
accession_numberDescriptionCode
widthDescriptionCode
IUPACDescriptionCode
ICDescriptionCode
get_stringDescriptionCode
idDescriptionCode
regexpDescriptionCode
regexp_arrayDescriptionCode
get_arrayDescriptionCode
_to_IUPACDescriptionCode
_to_consDescriptionCode
_calculate_consensusDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $site=new Bio::Matrix::PSM::SiteMatrix
              (-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,
               -IC=>$ic,-e_val=>$score, -id=>$mid);
 Function: Creates a new Bio::Matrix::PSM::SiteMatrix object from memory
 Throws  : If inconsistent data for all vectors (A,C,G and T) is provided,
           if you mix input types (string vs array) or if a position freq is 0.
 Example :
 Returns : Bio::Matrix::PSM::SiteMatrix object
 Args    : hash
next_poscodeprevnextTop
 Title   : next_pos
 Usage   : my %base=$site->next_pos;
 Function: 

           Retrieves the next position features: frequencies 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,base,prob,rel)
 Args    : none
curposcodeprevnextTop
 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_valcodeprevnextTop
 Title   : e_val
 Usage   : my $score=$site->e_val;
 Function: Gets/sets the e-value
 Throws  :
 Example :
 Returns : real number
 Args    : real number
consensuscodeprevnextTop
 Title   : consensus
 Usage   :  my $consensus=$site->consensus;
 Function: Returns the consensus
 Throws  :
 Example :
 Returns : string
 Args    :
accession_numbercodeprevnextTop
 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
widthcodeprevnextTop
 Title   : width
 Usage   : my $width=$site->width;
 Function: Returns the length of the site
 Throws  :
 Example :
 Returns : number
 Args    :
IUPACcodeprevnextTop
 Title   : IUPAC
 Usage   : my $iupac_consensus=$site->IUPAC;
 Function: Returns IUPAC compliant consensus
 Throws  :
 Example :
 Returns : string
 Args    :
ICcodeprevnextTop
 Title   : IC
 Usage   : my $ic=$site->IC;
 Function: Information content
 Throws  :
 Example :
 Returns : real number
 Args    : none
get_stringcodeprevnextTop
 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}
idcodeprevnextTop
 Title   : id
 Usage   : my $id=$site->id;
 Function: Gets/sets the site id
 Throws  :
 Example :
 Returns : string
 Args    : string
regexpcodeprevnextTop
 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_arraycodeprevnextTop
 Title   : regexp_array
 Usage   : my @regexp=$site->regexp;
 Function: Returns a regular expression which matches the IUPAC convention.
           N will match X, N, - and .
 Throws  :
 Example :
 Returns : array
 Args    :
 To do   : I have separated regexp and regexp_array, but
           maybe they can be rewritten as one - just check what
           should be returned
get_arraycodeprevnextTop
 Title   : get_array
 Usage   : my @freq_A=$site->get_array('A');
 Function: Returns an array with frequencies for a specified base
 Throws  :
 Example :
 Returns : array
 Args    : char
_to_IUPACcodeprevnextTop
 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_conscodeprevnextTop
 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_consensuscodeprevnextTop
 Title   : _calculate_consensus
 Usage   :
 Function: Internal stuff
 Throws  :
 Example :
 Returns :
 Args    :
Methods code
newdescriptionprevnextTop
sub new {
  my $self = shift;
  $self->throw_not_implemented();
}
next_posdescriptionprevnextTop
sub next_pos {
  my $self = shift;
  $self->throw_not_implemented();
}
curposdescriptionprevnextTop
sub curpos {
    my $self = shift;
   $self->throw_not_implemented();
}
e_valdescriptionprevnextTop
sub e_val {
    my $self = shift;
    $self->throw_not_implemented();
}
consensusdescriptionprevnextTop
sub consensus {
  my $self = shift;
  $self->throw_not_implemented();
}
accession_numberdescriptionprevnextTop
sub accession_number {
  my $self = shift;
  $self->throw_not_implemented();
}
widthdescriptionprevnextTop
sub width {
  my $self = shift;
  $self->throw_not_implemented();
}
IUPACdescriptionprevnextTop
sub IUPAC {
  my $self = shift;
  $self->throw_not_implemented();
}
ICdescriptionprevnextTop
sub IC {
my $self=shift;
$self->throw_not_implemented();
}
get_stringdescriptionprevnextTop
sub get_string {
 my $self=shift;
 $self->throw_not_implemented();
}
iddescriptionprevnextTop
sub id {
    my $self = shift;
    $self->throw_not_implemented();
}
regexpdescriptionprevnextTop
sub regexp {
 my $self=shift;
 $self->throw_not_implemented();
}
regexp_arraydescriptionprevnextTop
sub regexp_array {
 my $self=shift;
 $self->throw_not_implemented();
}
get_arraydescriptionprevnextTop
sub get_array {
  my $self=shift;
  $self->throw_not_implemented();
}
_to_IUPACdescriptionprevnextTop
sub _to_IUPAC {
    my $self = shift;
    $self->throw_not_implemented();
}
_to_consdescriptionprevnextTop
sub _to_cons {
    my $self = shift;
    $self->throw_not_implemented();
}
_calculate_consensusdescriptionprevnextTop
sub _calculate_consensus {
    my $self = shift;
    $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bio.perl.org/MailList.html     - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop