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

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