table of contents
TFBS::Matrix(3pm) | User Contributed Perl Documentation | TFBS::Matrix(3pm) |
NAME¶
TFBS::Matrix - base class for matrix patterns, containing methods common to allDESCRIPTION¶
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.comAPPENDIX¶
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
2016-12-17 | perl v5.24.1 |