| TFBS::Matrix(3pm) | User Contributed Perl Documentation | TFBS::Matrix(3pm) |
TFBS::Matrix - base class for matrix patterns, containing methods common to all
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.
Please send bug reports and other comments to the author.
Boris Lenhard <Boris.Lenhard@cgb.ki.se> Modified by Eivind Valen eivind.valen@gmail.com
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.
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
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
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
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
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
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
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
Title : randomize_columns Usage : $pfm->randomize_columns(); Function: Randomizes the columns of a matrix (in place). Returns : Nothing Args : none
| 2022-10-20 | perl v5.36.0 |