DESCRIPTION

TFBS::Matrix is a base class consisting of universal constructor called by its subclasses (TFBS::Matrix::*), and matrix manipulation methods that are independent of the matrix type. It is not meant to be instantiated itself.

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

Boris Lenhard <[email protected]> Modified by Eivind Valen [email protected]

APPENDIX

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

matrix

 Title   : matrix
 Usage   : my $matrix = $pwm->matrix();
           $pwm->matrix( [ [12, 3, 0, 0, 4, 0],
                           [ 0, 0, 0,11, 7, 0],
                           [ 0, 9,12, 0, 0, 0],
                           [ 0, 0, 0, 1, 1,12]
                         ]);
 Function: get/set for the matrix data
 Returns : a reference to 2D array of integers(PFM) or floats (ICM, PWM)
 Args    : none for get;
           a four line string, reference to 2D array, or a 2D piddle for set

pdl_matrix

 Title   : pdl_matrix
 Usage   : my $pdl = $pwm->pdl_matrix();
 Function: access the PDL matrix used to store the actual
           matrix data directly
 Returns : a PDL object, aka a piddle
 Args    : none

revcom

 Title   : revcom
 Usage   : my $revcom_pfm = $pfm->revcom();
 Function: create a matrix pattern object which is reverse complement
            of the current one
 Returns : a TFBS::Matrix::* object of the same type as the one
            the method acted upon
 Args    : none

rawprint

 Title   : rawprint
 Usage   : my $rawstring = $pfm->rawprint);
 Function: convert matrix data to a simple tab-separated format
 Returns : a four-line string of tab-separated integers or floats
 Args    : none

prettyprint

 Title   : prettyprint
 Usage   : my $prettystring = $pfm->prettyprint();
 Function: convert matrix data to a human-readable string format
 Returns : a four-line string with nucleotides and aligned numbers
 Args    : none

STAMPprint

 Title   : STAMPprint
 Usage   : my $STAMPstring = $pfm->STAMPprint();
 Function: Convert the matrix to STAMP readable format
 Returns : A string of the matrix in a TRANSFAC like format for STAMP
 Args    : none

length

 Title   : length
 Usage   : my $pattern_length = $pfm->length;
 Function: gets the pattern length in nucleotides
            (i.e. number of columns in the matrix)
 Returns : an integer
 Args    : none

randomize_columns

 Title   : randomize_columns
 Usage   : $pfm->randomize_columns();
 Function: Randomizes the columns of a matrix (in place).
 Returns : Nothing
 Args    : none