TFBS::Matrix(3pm)
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 actualmatrix 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 complementof 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