TFBS::MatrixSet(3pm)					User Contributed Perl Documentation				      TFBS::MatrixSet(3pm)

NAME

       TFBS::Matrix::Set - an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole

SYNOPSIS

	   # creation of a TFBS::MatrixSet object
	   # let @list_of_matrix_objects be a list of TFBS::Matrix::* objects

	   ###################################
	   # Create a TFBS::MatrixSet object:

	   my $matrixset = TFBS::MatrixSet->new(); # creates an empty set
	   $matrixset->add_Matrix(@list_of_matrix_objects); #add matrix objects to set
	   $matrixset->add_Matrix($matrixobj); # adds a single matrix object to set

	   # or, same as above:

	   my $matrixset = TFBS::MatrixSet->new(@list_of_matrix_objects, $matrixobj);

	   ###################################
	   #

DESCRIPTION

       TFBS::MatrixSet is an aggregate class storing a set of TFBS::Matrix::* subclass objects, and providing methods form manipulating those sets
       as a whole. TFBS::MatrixSet objects are created <I>de novo<I> or returned by some database (TFBS::DB::*) retrieval methods.

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.

   new
   add_matrix
	Title	: add_matrix
	Usage	: $matrixset->add_matrix(@list_of_matrix_objects);
	Function: Adds matrix objects to matrixset
	Returns : object reference (usually ignored)
	Args	: one or more TFBS::Matrix::* objects

   add_matrix_set
	Title	: add_matrix
	Usage	: $matrixset->add_matrix(@list_of_matrixset_objects);
	Function: Adds to the matrixset matrix objects contained in one or
		  more other matrixsets
	Returns : object reference (usually ignored)
	Args	: one or more TFBS::MatrixSet objects

   search_seq
	Title	: search_seq
	Usage	: my $siteset = $matrixset->search_seq(%args)
	Function: scans a nucleotide sequence with all patterns represented
		  stored in $matrixset;

		  It works only if all matrix objects in $matrixset understand
		  search_seq method (currently only TFBS::Matrix::PWM objects do)
	Returns : a TFBS::SiteSet object
	Args	: # you must specify either one of the following three:

		  -file,       # the name od a fasta file (single sequence)
		     #or
		  -seqobj      # a Bio::Seq object
			       # (more accurately, a Bio::PrimarySeqobject or a
			       #  subclass thereof)
		     #or
		  -seqstring # a string containing the sequence

		  -threshold,  # minimum score for the hit, either absolute
			       # (e.g. 11.2) or relative (e.g. "75%")
			       # OPTIONAL: default "80%"

   search_aln
	Title	: search_aln
	Usage	: my $site_pair_set = $matrixset->search_aln(%args)
	Function: Scans a pairwise alignment of nucleotide sequences
		  with the pattern represented by the PWM: it reports only
		  those hits that are present in equivalent positions of both
		  sequences and exceed a specified threshold score in both, AND
		  are found in regions of the alignment above the specified
		  conservation cutoff value.
		  It works only if all matrix object in $matrixset understand
		  search_aln method (currently only TFBS::Matrix::PWM objects do)

	Returns : a TFBS::SitePairSet object
	Args	: # you must specify either one of the following three:

		  -file,       # the name of the alignment file in Clustal
				      format
		     #or
		  -alignobj	 # a Bio::SimpleAlign object
			       # (more accurately, a Bio::PrimarySeqobject or a
			       #  subclass thereof)
		     #or
		  -alignstring # a multi-line string containing the alignment
			       # in clustal format
		  #############

		  -threshold,  # minimum score for the hit, either absolute
			       # (e.g. 11.2) or relative (e.g. "75%")
			       # OPTIONAL: default "80%"

		  -window,     # size of the sliding window (inn nucleotides)
			       # for calculating local conservation in the
			       # alignment
			       # OPTIONAL: default 50

		  -cutoff      # conservation cutoff (%) for including the
			       # region in the results of the pattern search
			       # OPTIONAL: default "70%"

		  -subpart     # subpart of the alignment to search, given as e.g.
			       # -subpart => { relative_to => 1,
			       #	       start	   => 140,
			       #	       end	   => 180 }
			       # where start and end are coordinates in the
			       # sequence indicated by relative_to (1 for the
			       # 1st sequence in the alignment, 2 for the 2nd)
			       # OPTIONAL: by default searches entire alignment

		  -conservation
			       # conservation profile, a TFBS::ConservationProfile
			       # OPTIONAL: by default the conservation profile is
			       # computed internally on the fly (less efficient)

   size
	Title	: size
	Usage	: my $number_of_matrices = $matrixset->size;
	Function: gets the number of matrix objects in the $matrixset
		  (i.e. the size of the set)
	Returns : a number
	Args	: none

   Iterator
	Title	: Iterator
	Usage	: my $matrixset_iterator =
			  $matrixset->Iterator(-sort_by =>'total_ic');
		  while (my $matrix_object = $matrix_iterator->next) {
		      # do whatever you want with individual matrix objects
		  }
	Function: Returns an iterator object that can be used to go through
		  all members of the set
	Returns : an iterator object (currently undocumentened in TFBS -
				      but understands the 'next' method)
	Args	: -sort_by # optional - currently it accepts
			   #	'ID' (alphabetically)
			   #	'name' (alphabetically)
			   #	'class' (alphabetically)
			   #	'total_ic' (numerically, decreasing order)

		  -reverse # optional - reverses the default sorting order if true

   randomize_columns
	Title	: randomize_columns
	Usage	: $matrixset->randomize_columns();
	Function: Randomizes the columns between all the matrices in the set
	Returns : nothing
	Args	: none

perl v5.14.2							    2008-01-24						      TFBS::MatrixSet(3pm)