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.\" ========================================================================
.\"
.IX Title "TFBS::MatrixSet 3pm"
.TH TFBS::MatrixSet 3pm "2008-01-24" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
TFBS::Matrix::Set \- an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # 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);
\&
\&    ###################################
\&    #
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
Modified by Eivind Valen eivind.valen@gmail.com
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "new"
.IX Subsection "new"
.SS "add_matrix"
.IX Subsection "add_matrix"
.Vb 5
\& 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
.Ve
.SS "add_matrix_set"
.IX Subsection "add_matrix_set"
.Vb 6
\& 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
.Ve
.SS "search_seq"
.IX Subsection "search_seq"
.Vb 4
\& 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%"
.Ve
.SS "search_aln"
.IX Subsection "search_aln"
.Vb 10
\& 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)
.Ve
.SS "size"
.IX Subsection "size"
.Vb 6
\& 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
.Ve
.SS "Iterator"
.IX Subsection "Iterator"
.Vb 10
\& Title   : Iterator
\& Usage   : my $matrixset_iterator =
\&                   $matrixset\->Iterator(\-sort_by =>\*(Aqtotal_ic\*(Aq);
\&           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 \*(Aqnext\*(Aq method)
\& Args    : \-sort_by # optional \- currently it accepts
\&                    #    \*(AqID\*(Aq (alphabetically)
\&                    #    \*(Aqname\*(Aq (alphabetically)
\&                    #    \*(Aqclass\*(Aq (alphabetically)
\&                    #    \*(Aqtotal_ic\*(Aq (numerically, decreasing order)
\&
\&           \-reverse # optional \- reverses the default sorting order if true
.Ve
.SS "randomize_columns"
.IX Subsection "randomize_columns"
.Vb 5
\& Title   : randomize_columns
\& Usage   : $matrixset\->randomize_columns();
\& Function: Randomizes the columns between all the matrices in the set
\& Returns : nothing
\& Args    : none
.Ve