TFBS::MatrixSet(3pm)

📦
version 0.7.1 · 6 versions
, in ubuntu stonking

okay bestie, pull up a chair 🎀 this is the TFBS::MatrixSet(3pm) page from the User Contributed Perl Documentation, and it is exactly as iconic as it sounds. no cap.

✨ NAME ✨

TFBS::Matrix::Set — an aggregate class that represents a whole set of matrix patterns, and it's packing all the methods you need to mess with that set as one big beautiful unit 💅

🌸 SYNOPSIS 🌸

okay so here's the vibe, fr fr:

    # 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 that stores a whole set of TFBS::Matrix::* subclass objects and hands you the methods to manipulate those sets as one glorious whole. The way that it works? You either create TFBS::MatrixSet objects de novo, or some database retrieval method (TFBS::DB::*) just hands one back to you like a little gift 🎁

💌 FEEDBACK 💌

Found a bug? Got thoughts? Send those bug reports and other comments straight to the author, bestie 🫶

👑 AUTHOR - Boris Lenhard 👑

Boris Lenhard <Boris.Lenhard@cgb.ki.se> — and modified by Eivind Valen <eivind.valen@gmail.com> ✨

📎 APPENDIX 📎

The rest of this doc spills the tea on every single object method, ok? Internal methods are the ones preceded with an underscore, so you can clock them instantly 🙈

new

literally just vibes, no docs listed here 💀

new2

same energy, no extra deets, moving on 💅

add_matrix

  • Title: add_matrix
  • Usage: $matrixset->add_matrix(@list_of_matrix_objects);
  • Function: adds matrix objects to the matrixset
  • Returns: an object reference (which you're usually gonna ignore, ngl)
  • 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 the matrix objects contained in one or more other matrixsets
  • Returns: an object reference (again, 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 the patterns stored in $matrixset.
heads up: this only works if all the matrix objects in $matrixset understand the search_seq method — and rn, only TFBS::Matrix::PWM objects do.
  • Returns: a TFBS::SiteSet object
  • Args: you have to specify exactly one of these three 👇
  • -file — the name of a fasta file (single sequence)
  • -seqobj — a Bio::Seq object (or, more accurately, a Bio::PrimarySeq object or a subclass thereof)
  • -seqstring — a string containing the sequence

and then this one:

  • -threshold — minimum score for the hit, either absolute (like 11.2) or relative (like "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, exceed a specified threshold score in both, AND are found in regions of the alignment that are above the specified conservation cutoff value. Obsessed with the specificity honestly 👑
heads up again: this only works if all matrix objects in $matrixset understand the search_aln method — currently only TFBS::Matrix::PWM objects do.
  • Returns: a TFBS::SitePairSet object
  • Args: you must specify exactly one of these three 👇
  • -file — the name of the alignment file in Clustal format
  • -alignobj — a Bio::SimpleAlign object (or, more accurately, a Bio::PrimarySeq object or a subclass thereof)
  • -alignstring — a multi-line string containing the alignment in clustal format

and then the rest:

  • -threshold — minimum score for the hit, either absolute (like 11.2) or relative (like "75%"). OPTIONAL: default "80%"
  • -window — size of the sliding window (in nucleotides) used to calculate local conservation in the alignment. OPTIONAL: default 50
  • -cutoff — conservation cutoff (%) for including a region in the results of the pattern search. OPTIONAL: default "70%"
  • -subpart — a subpart of the alignment to search, given like this:
    -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 it searches the entire alignment.

  • -conservation — a conservation profile, a TFBS::ConservationProfile. OPTIONAL: by default the conservation profile is computed internally on the fly (which is less efficient, ngl).

size

  • Title: size
  • Usage: my $number_of_matrices = $matrixset->size;
  • Function: gets the number of matrix objects in the $matrixset (aka the size of the set, duh)
  • 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 you can use to go through every single member of the set, one by one, no skipping 💅
  • Returns: an iterator object (currently undocumented in TFBS — but it understands the next method, iykyk)
  • 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, so watch out 👀)
  • 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, and an array of TFBS::MatrixSets, one for each cluster 🎀
  • Args: many, bestie:
    • -stampdir — the directory where stamp is located. Not necessary if it's in the PATH.
    • -tempdir — directory to put temporary files in. Defaults to "/tmp".
    • -noclean — 0 to clean up temporary files, 1 otherwise
    • -tree — method for constructing the tree (UPGMA/SOTA). Default: 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 — the directory where stamp is located. Not necessary if it's in the PATH.
    • -tempdir — directory to put temporary files in. Defaults to "/tmp".
    • -noclean — 0 to clean up temporary files, 1 otherwise
    • -align — alignment method

and that's the whole page, bestie!! this gorgeous thing is perl v5.42.3, dated 2026-08-21, and it's giving TFBS::MatrixSet(3pm) energy from start to finish 💖✨ go forth and manipulate your matrix sets, you absolute main character 🦋👑

📦 where this page comes from