NAME¶
TFBS::Matrix - base class for matrix patterns, containing methods common to all
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 <Boris.Lenhard@cgb.ki.se> Modified by Eivind Valen
eivind.valen@gmail.com
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
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
Returns : Nothing
Args : none