tfbs::matrix(3pm) [debian man page]
TFBS::Matrix(3pm) User Contributed Perl Documentation 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 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 perl v5.14.2 2008-01-24 TFBS::Matrix(3pm)
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TFBS::Matrix::ICM(3pm) User Contributed Perl Documentation TFBS::Matrix::ICM(3pm) NAME
TFBS::Matrix::ICM - class for information content matrices of nucleotide patterns SYNOPSIS
o creating a TFBS::Matrix::ICM object manually: my $matrixref = [ [ 0.00, 0.30, 0.00, 0.00, 0.24, 0.00 ], [ 0.00, 0.00, 0.00, 1.45, 0.42, 0.00 ], [ 0.00, 0.89, 2.00, 0.00, 0.00, 0.00 ], [ 0.00, 0.00, 0.00, 0.13, 0.06, 2.00 ] ]; my $icm = TFBS::Matrix::ICM->new(-matrix => $matrixref, -name => "MyProfile", -ID => "M0001" ); # or my $matrixstring = <<ENDMATRIX 2.00 0.30 0.00 0.00 0.24 0.00 0.00 0.00 0.00 1.45 0.42 0.00 0.00 0.89 2.00 0.00 0.00 0.00 0.00 0.00 0.00 0.13 0.06 2.00 ENDMATRIX ; my $icm = TFBS::Matrix::ICM->new(-matrixstring => $matrixstring, -name => "MyProfile", -ID => "M0001" ); o retrieving a TFBS::Matix::ICM object from a database: (See documentation of individual TFBS::DB::* modules to learn how to connect to different types of pattern databases and retrieve TFBS::Matrix::* objects from them.) my $db_obj = TFBS::DB::JASPAR2->new (-connect => ["dbi:mysql:JASPAR2:myhost", "myusername", "mypassword"]); my $pfm = $db_obj->get_Matrix_by_ID("M0001", "ICM"); # or my $pfm = $db_obj->get_Matrix_by_name("MyProfile", "ICM"); o retrieving list of individual TFBS::Matrix::ICM objects from a TFBS::MatrixSet object (see decumentation of TFBS::MatrixSet to learn how to create objects for storage and manipulation of multiple matrices) my @icm_list = $matrixset->all_patterns(-sort_by=>"name"); * drawing a sequence logo $icm->draw_logo(-file=>"logo.png", -full_scale =>2.25, -xsize=>500, -ysize =>250, -graph_title=>"C/EBPalpha binding site logo", -x_title=>"position", -y_title=>"bits"); DESCRIPTION
TFBS::Matrix::ICM is a class whose instances are objects representing position weight matrices (PFMs). An ICM is normally calculated from a raw position frequency matrix (see TFBS::Matrix::PFM for the explanation of position frequency matrices). For example, given the following position frequency matrix, A:[ 12 3 0 0 4 0 ] C:[ 0 0 0 11 7 0 ] G:[ 0 9 12 0 0 0 ] T:[ 0 0 0 1 1 12 ] the standard computational procedure is applied to convert it into the following information content matrix: A:[2.00 0.30 0.00 0.00 0.24 0.00] C:[0.00 0.00 0.00 1.45 0.42 0.00] G:[0.00 0.89 2.00 0.00 0.00 0.00] T:[0.00 0.00 0.00 0.13 0.06 2.00] which contains the "weights" associated with the occurence of each nucleotide at the given position in a pattern. A TFBS::Matrix::PWM object is equipped with methods to search nucleotide sequences and pairwise alignments of nucleotide sequences with the pattern they represent, and return a set of sites in nucleotide sequence (a TFBS::SiteSet object for single sequence search, and a TFBS::SitePairSet for the alignment search). FEEDBACK
Please send bug reports and other comments to the author. AUTHOR - Boris Lenhard Boris Lenhard <Boris.Lenhard@cgb.ki.se> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. new Title : new Usage : my $icm = TFBS::Matrix::ICM->new(%args) Function: constructor for the TFBS::Matrix::ICM object Returns : a new TFBS::Matrix::ICM object Args : # you must specify either one of the following three: -matrix, # reference to an array of arrays of integers #or -matrixstring,# a string containing four lines # of tab- or space-delimited integers #or -matrixfile, # the name of a file containing four lines # of tab- or space-delimited integers ####### -name, # string, OPTIONAL -ID, # string, OPTIONAL -class, # string, OPTIONAL -tags # an array reference, OPTIONAL to_PWM Title : to_PWM Usage : my $pwm = $icm->to_PWM() Function: converts an information content matrix (a TFBS::Matrix::ICM object) to position weight matrix. At present it assumes uniform background distribution of nucleotide frequencies. Returns : a new TFBS::Matrix::PWM object Args : none; in the future releases, it should be able to accept a user defined background probability of the four nucleotides draw_logo Title : draw_logo Usage : my $gdImageObj = $icm->draw_logo(%args) Function: Draws a "sequence logo", a graphical representation of a possibly degenerate fixed-width nucleotide sequence pattern, from the information content matrix Returns : a GD::Image object; if you only need the image file you can ignore it Args : -file, # the name of the output PNG image file # OPTIONAL: default none -xsize # width of the image in pixels # OPTIONAL: default 600 -ysize # height of the image in pixels # OPTIONAL: default 5/8 of -x_size -startpos # start position in the logo for x axis # OPTIONAL: default is 1 -margin # size of image margins in pixels # OPTIONAL: default 15% of -y_size -full_scale # the maximum value on the y-axis, in bits # OPTIONAL: default 2.25 -graph_title,# the graph title # OPTIONAL: default none -x_title, # x-axis title; OPTIONAL: default none -y_title # y-axis title; OPTIONAL: default none -error_bars # reference to an array of S.D. values for each column; OPTIONAL -ps # if true, produces a postscript string instead of a GD::Image object -pdf # if true AND the -file argumant is used, produces an output pdf file _draw_ps_logo Title : _draw_ps_logo Usage : my $postscript_string = $icm->_draw_ps_logo(%args) Internal method, should be accessed using draw_logo() Function: Draws a "sequence logo", a graphical representation of a possibly degenerate fixed-width nucleotide sequence pattern, from the information content matrix Returns : a postscript string; if you only need the image file you can ignore it Args : -file, # the name of the output PNG image file # OPTIONAL: default none -xsize # width of the image in pixels # OPTIONAL: default 600 -ysize # height of the image in pixels # OPTIONAL: default 5/8 of -x_size -full_scale # the maximum value on the y-axis, in bits # OPTIONAL: default 2.25 -graph_title,# the graph title # OPTIONAL: default none -x_title, # x-axis title; OPTIONAL: default none -y_title # y-axis title; OPTIONAL: default none _draw_svg_logo name ID class matrix length revcom rawprint prettyprint The above methods are common to all matrix objects. Please consult TFBS::Matrix to find out how to use them. perl v5.14.2 2008-01-24 TFBS::Matrix::ICM(3pm)