TFBS::TFFM(3pm)

✨ TFBS::TFFM ✨

okay so bestie, welcome to the TFBS::TFFM page in the User Contributed Perl Documentation section 💖 this is the whole vibe: a little Perl class that holds info about TFFMs (Transcription Factor Flexible Models). let's get into it 🦋

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🌸 NAME 🌸

TFBS::TFFM — a class for Transcription Factor Flexible Models (TFFMs). periodt. 👑

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💫 DESCRIPTION 💫

TFBS::TFFM is a class whose whole job is holding the basic info about a TFFM. main character energy for metadata, honestly.

it was mainly designed to store the info about a TFFM the way it's stored in the TFFM table of the JASPAR DB, which got newly introduced in the JASPAR 2016 version. slay.

🚨 BUT. listen. it does NOT (currently) store the actual XML that describes the model. not yet! it would be simple to add though, so like… noted. 📝

at the time of this writing, the relationship between JASPAR matrices (as stored in the MATRIX table) and TFFMs was not completely clear, and the matrix IDs related to a TFFM are stored in the TFFM table. the relationship could be 1:n, m:1 or m:n in the future, so this may well be changed and a joining table created to facilitate this. the plot thickens, iykyk 🙈

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🫶 FEEDBACK 🫶

please send bug reports and other comments to the author. they're literally waiting. 💌

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👑 AUTHOR - David Arenillas 👑

David Arenillas: dave@cmmt.ubc.ca

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods, one by one, no skips. internal methods are preceded with an underscore. 💅

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🔖 ID

• Title : ID
• Usage :

my $id = $tffm->ID();

• Function: get/set the ID of this TFFM.
• Returns : The ID of this TFFM.
• Args : None for get, or a new string ID.

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🎀 name

• Title : name
• Usage :

my $name = $tffm->name();

• Function: get/set the name of the transcription factor for which this TFFM was modelled.
• Returns : Name of the TF modelled by this TFFM.
• Args : None for get, or a new string TF name.

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🧪 experiment_name

• Title : experiment_name
• Usage :

my $filename = $tffm->experiment_name();

• Function: get/set the name of the experimental data on which this TFFM (generally ChIP-seq peak data) was trained. often this is the base file name of the ChIP-seq peaks file. very "tell me where you came from" of it.
• Returns : Name of the experiment/datafile.
• Args : None for get, or a new experiment/datafile name.

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🍓 log_p_1st_order

• Title : log_p_1st_order
• Usage :

my $log_p_val = $tffm->log_p_1st_order();

• Function: get/set the log(p) value for the 1st order model of this TFFM.
• Returns : Log(p) value of the 1st-order model.
• Args : None for get, or a new 1st-order log(p) value.

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🔥 log_p_detailed

• Title : log_p_detailed
• Usage :

my $log_p_val = $tffm->log_p_detailed();

• Function: get/set the log(p) value for the detailed model of this TFFM.
• Returns : Log(p) value of the detailed model.
• Args : None for get, or a new detailed log(p) value.

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🌈 matrix_ID

• Title : matrix_ID
• Usage :

my $matrix_id = $tffm->matrix_ID();

• Function: get/set the ID of the matrix associated to this TFFM.
• Returns : ID of the matrix associated to this TFFM.
• Args : None for get, or a JASPAR matrix ID.

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🦋 matrix

• Title : matrix
• Usage :

my $matrix = $tffm->matrix();

• Function: get/set the matrix object related to this TFFM.
• Returns : A reference to a TFBS::Matrix object which was used to train the TFFM.
• Args : None for get, or a new TFBS::Matrix object reference.

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and that's the whole page, bestie 💜 this was perl v5.42.3, dated 2026-08-21, and the manual name was TFBS::TFFM(3pm) — iconic, no notes, bye 🎀✨