Provided by: libtfbs-perl_0.7.1-2_amd64 bug

NAME

       TFBS::Matrix::PWM - class for position weight matrices of nucleotide patterns

SYNOPSIS

       ·   creating a TFBS::Matrix::PWM object manually:

               my $matrixref = [ [ 0.61, -3.16,  1.83, -3.16,  1.21, -0.06],
                                 [-0.15, -2.57, -3.16, -3.16, -2.57, -1.83],
                                 [-1.57,  1.85, -2.57, -1.34, -1.57,  1.14],
                                 [ 0.31, -3.16, -2.57,  1.76,  0.24, -0.83]
                               ];
               my $pwm = TFBS::Matrix::PWM->new(-matrix => $matrixref,
                                                -name   => "MyProfile",
                                                -ID     => "M0001"
                                               );
               # or

               my $matrixstring = <<ENDMATRIX
                0.61 -3.16  1.83 -3.16  1.21 -0.06
               -0.15 -2.57 -3.16 -3.16 -2.57 -1.83
               -1.57  1.85 -2.57 -1.34 -1.57  1.14
                0.31 -3.16 -2.57  1.76  0.24 -0.83
               ENDMATRIX
               ;
               my $pwm = TFBS::Matrix::PWM->new(-matrixstring => $matrixstring,
                                                -name         => "MyProfile",
                                                -ID           => "M0001"
                                               );

       ·   retrieving a TFBS::Matix::PWM object from a database:

           (See documentation of individual TFBS::DB::* modules to learn how to connect to
           different types of pattern databases and retrieve TFBS::Matrix::* objects from them.)

               my $db_obj = TFBS::DB::JASPAR2->new
                               (-connect => ["dbi:mysql:JASPAR2:myhost",
                                             "myusername", "mypassword"]);
               my $pwm = $db_obj->get_Matrix_by_ID("M0001", "PWM");
               # or
               my $pwm = $db_obj->get_Matrix_by_name("MyProfile", "PWM");

       ·   retrieving list of individual TFBS::Matrix::PWM objects from a TFBS::MatrixSet object

           (see decumentation of TFBS::MatrixSet to learn how to create objects for storage and
           manipulation of multiple matrices)

               my @pwm_list = $matrixset->all_patterns(-sort_by=>"name");

       ·   scanning a nucleotide sequence with a matrix

               my $siteset = $pwm->search_seq(-file      =>"myseq.fa",
                                              -threshold => "80%");

       ·   scanning a pairwise alignment with a matrix

               my $site_pair_set = $pwm->search_aln(-file      =>"myalign.aln",
                                                    -threshold => "80%",
                                                    -cutoff    => "70%",
                                                    -window    => 50);

DESCRIPTION

       TFBS::Matrix::PWM is a class whose instances are objects representing position weight
       matrices (PWMs). A PWM is normally calculated from a raw position frequency matrix (see
       TFBS::Matrix::PFM for the explanation of position frequency matrices). For example, given
       the following position frequency matrix:

           A:[ 12     3     0     0     4     0  ]
           C:[  0     0     0    11     7     0  ]
           G:[  0     9    12     0     0     0  ]
           T:[  0     0     0     1     1    12  ]

       The standard computational procedure is applied to convert it into the following position
       weight matrix:

           A:[ 0.61 -3.16  1.83 -3.16  1.21 -0.06]
           C:[-0.15 -2.57 -3.16 -3.16 -2.57 -1.83]
           G:[-1.57  1.85 -2.57 -1.34 -1.57  1.14]
           T:[ 0.31 -3.16 -2.57  1.76  0.24 -0.83]

       which contains the "weights" associated with the occurrence of each nucleotide at the
       given position in a pattern.

       A TFBS::Matrix::PWM object is equipped with methods to search nucleotide sequences and
       pairwise alignments of nucleotide sequences with the pattern they represent, and return a
       set of sites in nucleotide sequence (a TFBS::SiteSet object for single sequence search,
       and a TFBS::SitePairSet for the alignment search).

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       preceded with an underscore.

   new
        Title   : new
        Usage   : my $pwm = TFBS::Matrix::PWM->new(%args)
        Function: constructor for the TFBS::Matrix::PWM object
        Returns : a new TFBS::Matrix::PWM object
        Args    : # you must specify either one of the following three:

                  -matrix,      # reference to an array of arrays of integers
                     #or
                  -matrixstring,# a string containing four lines
                                # of tab- or space-delimited integers
                     #or
                  -matrixfile,  # the name of a file containing four lines
                                # of tab- or space-delimited integers
                  #######

                  -name,        # string, OPTIONAL
                  -ID,          # string, OPTIONAL
                  -class,       # string, OPTIONAL
                  -tags         # an array reference, OPTIONAL

   search_seq
        Title   : search_seq
        Usage   : my $siteset = $pwm->search_seq(%args)
        Function: scans a nucleotide sequence with the pattern represented
                  by the PWM
        Returns : a TFBS::SiteSet object
        Args    : # you must specify either one of the following three:

                  -file,       # the name od a fasta file (single sequence)
                     #or
                  -seqobj      # a Bio::Seq object
                               # (more accurately, a Bio::PrimarySeqobject or a
                               #  subclass thereof)
                     #or
                  -seqstring # a string containing the sequence

                  -threshold,  # minimum score for the hit, either absolute
                               # (e.g. 11.2) or relative (e.g. "75%")
                               # OPTIONAL: default "80%"

                  -subpart     # subpart of the sequence to search, given as
                               # -subpart => { start => 140,
                               #               end   => 180 }
                               # where start and end are coordinates in the
                               # sequence; the coordinate range is interpreted
                               # in the BioPerl tradition (1-based, inclusive)
                               # OPTIONAL: by default searches entire alignment

   search_aln
        Title   : search_aln
        Usage   : my $site_pair_set = $pwm->search_aln(%args)
        Function: Scans a pairwise alignment of nucleotide sequences
                  with the pattern represented by the PWM: it reports only
                  those hits that are present in equivalent positions of both
                  sequences and exceed a specified threshold score in both, AND
                  are found in regions of the alignment above the specified
                  conservation cutoff value.
        Returns : a TFBS::SitePairSet object
        Args    : # you must specify either one of the following three:

                  -file,       # the name of the alignment file in Clustal
                                      format
                     #or
                  -alignobj      # a Bio::SimpleAlign object
                               # (more accurately, a Bio::PrimarySeqobject or a
                               #  subclass thereof)
                     #or
                  -alignstring # a multi-line string containing the alignment
                               # in clustal format
                  #############

                  -threshold,  # minimum score for the hit, either absolute
                               # (e.g. 11.2) or relative (e.g. "75%")
                               # OPTIONAL: default "80%"

                  -window,     # size of the sliding window (inn nucleotides)
                               # for calculating local conservation in the
                               # alignment
                               # OPTIONAL: default 50

                  -cutoff      # conservation cutoff (%) for including the
                               # region in the results of the pattern search
                               # OPTIONAL: default "70%"

                  -subpart     # subpart of the alignment to search, given as e.g.
                               # -subpart => { relative_to => 1,
                               #               start       => 140,
                               #               end         => 180 }
                               # where start and end are coordinates in the
                               # sequence indicated by relative_to (1 for the
                               # 1st sequence in the alignment, 2 for the 2nd)
                               # OPTIONAL: by default searches entire alignment

                  -conservation
                               # conservation profile, a TFBS::ConservationProfile
                               # OPTIONAL: by default the conservation profile is
                               # computed internally on the fly (less efficient)

   name
   ID
   class
   matrix
   length
   revcom
   rawprint
   prettyprint
       The above methods are common to all matrix objects. Please consult TFBS::Matrix to find
       out how to use them.