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.\" ========================================================================
.\"
.IX Title "TFBS::MatrixSet 3"
.TH TFBS::MatrixSet 3 "2005-01-04" "perl v5.12.4" "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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.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>
.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
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