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.\" ========================================================================
.\"
.IX Title "TFBS::TFFM 3pm"
.TH TFBS::TFFM 3pm "2018-11-02" "perl v5.28.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::TFFM \- class for Transcription Factor Flexible Models (TFFMs)
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1TFBS::TFFM\s0 is a class to hold basic information about a \s-1TFFM.\s0 It was
mainly designed to store the information about a \s-1TFFM\s0 stored in the
\&\s-1TFFM\s0 table of the \s-1JASPAR DB\s0 newly introduced in the \s-1JASPAR 2016\s0 version.
It does \s-1NOT\s0 (currently) store the actual \s-1XML\s0 describing the the model but
this would be simple to add. At the time of this writing the relationship 
between \s-1JASPAR\s0 matrices as stored in the \s-1MATRIX\s0 table and TFFMs was not
completely clear and the matrix IDs related to a \s-1TFFM\s0 are stored in the
\&\s-1TFFM\s0 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 "\s-1ID\s0"
.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