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.IX Title "TFBS::TFFM 3pm"
.TH TFBS::TFFM 3pm 2024-03-13 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
TFBS::TFFM \- class for Transcription Factor Flexible Models (TFFMs)
.SH DESCRIPTION
.IX Header "DESCRIPTION"
TFBS::TFFM is a class to hold basic information about a TFFM. It was
mainly designed to store the information about a TFFM stored in the
TFFM table of the JASPAR DB newly introduced in the JASPAR 2016 version.
It does NOT (currently) store the actual XML describing the the model but
this would be simple to add. 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.
.SH FEEDBACK
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- David Arenillas"
.IX Header "AUTHOR - David Arenillas"
David Arenillas: dave@cmmt.ubc.ca
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS ID
.IX Subsection "ID"
.Vb 2
\& 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.
.Ve
.SS name
.IX Subsection "name"
.Vb 2
\& 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.
.Ve
.SS experiment_name
.IX Subsection "experiment_name"
.Vb 2
\& 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) TFFM was trained. Often this
\&           is base file name of ChIP\-seq peaks file.
\& Returns : Name of the experiment/datafile.
\& Args    : None for get or a new experiment/datafile name.
.Ve
.SS log_p_1st_order
.IX Subsection "log_p_1st_order"
.Vb 2
\& 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.
.Ve
.SS log_p_detailed
.IX Subsection "log_p_detailed"
.Vb 2
\& 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.
.Ve
.SS matrix_ID
.IX Subsection "matrix_ID"
.Vb 2
\& 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.
.Ve
.SS matrix
.IX Subsection "matrix"
.Vb 2
\& Title   : matrix
\& Usage   : my $matrix = $tffm\->matrix();
\&
\& Function: Get/set the matrix object related to this TFFM
\& Returns : A reference to TFBS::Matrix object which was used to train the
\&           TFFM.
\& Args    : None for get or a new TFBS::Matrix object reference.
.Ve