Linux Certif

Toute la documentation sur la certification Linux LPI

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