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

NAME

       TFBS::Matrix::ICM - class for information content matrices of nucleotide patterns

SYNOPSIS

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

               my $matrixref = [ [ 0.00, 0.30, 0.00, 0.00, 0.24, 0.00 ],
                                 [ 0.00, 0.00, 0.00, 1.45, 0.42, 0.00 ],
                                 [ 0.00, 0.89, 2.00, 0.00, 0.00, 0.00 ],
                                 [ 0.00, 0.00, 0.00, 0.13, 0.06, 2.00 ]
                               ];
               my $icm = TFBS::Matrix::ICM->new(-matrix => $matrixref,
                                                -name   => "MyProfile",
                                                -ID     => "M0001"
                                               );

               # or

               my $matrixstring = <<ENDMATRIX
               2.00   0.30   0.00   0.00   0.24   0.00
               0.00   0.00   0.00   1.45   0.42   0.00
               0.00   0.89   2.00   0.00   0.00   0.00
               0.00   0.00   0.00   0.13   0.06   2.00
               ENDMATRIX
               ;
               my $icm = TFBS::Matrix::ICM->new(-matrixstring => $matrixstring,
                                                -name         => "MyProfile",
                                                -ID           => "M0001"
                                               );

       ·   retrieving a TFBS::Matix::ICM 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 $pfm = $db_obj->get_Matrix_by_ID("M0001", "ICM");
               # or
               my $pfm = $db_obj->get_Matrix_by_name("MyProfile", "ICM");

       ·   retrieving list of individual TFBS::Matrix::ICM 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 @icm_list = $matrixset->all_patterns(-sort_by=>"name");

           * drawing a sequence logo

               $icm->draw_logo(-file=>"logo.png",
                               -full_scale =>2.25,
                               -xsize=>500,
                               -ysize =>250,
                               -graph_title=>"C/EBPalpha binding site logo",
                               -x_title=>"position",
                               -y_title=>"bits");

DESCRIPTION

       TFBS::Matrix::ICM is a class whose instances are objects representing position weight
       matrices (PFMs). An ICM 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
       information content matrix:

           A:[2.00  0.30  0.00  0.00  0.24  0.00]
           C:[0.00  0.00  0.00  1.45  0.42  0.00]
           G:[0.00  0.89  2.00  0.00  0.00  0.00]
           T:[0.00  0.00  0.00  0.13  0.06  2.00]

       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 $icm = TFBS::Matrix::ICM->new(%args)
        Function: constructor for the TFBS::Matrix::ICM object
        Returns : a new TFBS::Matrix::ICM 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

   to_PWM
        Title   : to_PWM
        Usage   : my $pwm = $icm->to_PWM()
        Function: converts an  information content matrix (a TFBS::Matrix::ICM object)
                  to position weight matrix. At present it assumes uniform
                  background distribution of nucleotide frequencies.
        Returns : a new TFBS::Matrix::PWM object
        Args    : none; in the future releases, it should be able to accept
                  a user defined background probability of the four
                  nucleotides

   draw_logo
        Title   : draw_logo
        Usage   : my $gdImageObj = $icm->draw_logo(%args)
        Function: Draws a "sequence logo", a graphical representation
                  of a possibly degenerate fixed-width nucleotide
                  sequence pattern, from the information content matrix
        Returns : a GD::Image object;
                  if you only need the image file you can ignore it
        Args    : -file,       # the name of the output PNG image file
                               # OPTIONAL: default none
                  -xsize       # width of the image in pixels
                               # OPTIONAL: default 600
                  -ysize       # height of the image in pixels
                               # OPTIONAL: default 5/8 of -x_size
                  -startpos    # start position in the logo for x axis
                               # OPTIONAL: default is 1
                  -margin      # size of image margins in pixels
                               # OPTIONAL: default 15% of -y_size
                  -full_scale  # the maximum value on the y-axis, in bits
                               # OPTIONAL: default 2.25
                  -graph_title,# the graph title
                               # OPTIONAL: default none
                  -x_title,    # x-axis title; OPTIONAL: default none
                  -y_title     # y-axis title; OPTIONAL: default none
                  -error_bars  # reference to an array of S.D. values for each column; OPTIONAL
                  -ps          # if true, produces a postscript string instead of a GD::Image object
                   -pdf          # if true AND the -file argumant is used, produces an output pdf file

   _draw_ps_logo
        Title   : _draw_ps_logo
        Usage   : my $postscript_string = $icm->_draw_ps_logo(%args)
                  Internal method, should be accessed using draw_logo()
        Function: Draws a "sequence logo", a graphical representation
                  of a possibly degenerate fixed-width nucleotide
                  sequence pattern, from the information content matrix
        Returns : a postscript string;
                  if you only need the image file you can ignore it
        Args    : -file,       # the name of the output PNG image file
                               # OPTIONAL: default none
                  -xsize       # width of the image in pixels
                               # OPTIONAL: default 600
                  -ysize       # height of the image in pixels
                               # OPTIONAL: default 5/8 of -x_size
                  -full_scale  # the maximum value on the y-axis, in bits
                               # OPTIONAL: default 2.25
                  -graph_title,# the graph title
                               # OPTIONAL: default none
                  -x_title,    # x-axis title; OPTIONAL: default none
                  -y_title     # y-axis title; OPTIONAL: default none

   _draw_svg_logo
   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.