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.
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 (in place).
Returns : nothing
Args : none
remove_Matrix_by_ID¶
Title : remove_Matrix_by_ID
Usage : $matrixset->remove_Matrix_by_ID($id);
Function: Removes a matrix from the set
Returns : Nothing
Args : None
cluster¶
Title : cluster
Usage : $matrixset->cluster(%args)
Function: Clusters the matrices in the set
Returns : The root node of the hierarchical clustering tree.
An integer specifying the optimal number of clusters.
An array of TFBS::MatrixSets, one for each cluster.
Args : Many:
-stampdir Directory where stamp is located. Not necessary if it is in the PATH.
-tempdir Directory to put temporary files. Defaults to "/tmp"
-noclean 0 to clean up temporary files, 1 otherwise
-tree Method for constructing tree (UPGMA/SOTA). Def:UPGMA
fbp¶
Title : fbp
Usage : $matrixset->fbp(%args);
Function: Creates a familial binding profile (FBP) for the set
Returns : A familial binding profile represented as a TFBS::Matrix::PFM
Args : Many
-stampdir Directory where stamp is located. Not necessary if it is in the PATH.
-tempdir Directory to put temporary files. Defaults to "/tmp"
-noclean 0 to clean up temporary files, 1 otherwise
-align Alignment method
