.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::Map::TranscriptionFactor 3pm"
.TH Bio::Map::TranscriptionFactor 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Map::TranscriptionFactor \- A transcription factor modelled as a mappable
element
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  use Bio::Map::TranscriptionFactor;
\&  use Bio::Map::GeneMap;
\&  use Bio::Map::Position;
\&
\&  # model a TF that binds 500bp upstream of the BRCA2 gene in humans and
\&  # 250bp upstream of BRCA2 in mice
\&  my $tf = Bio::Map::TranscriptionFactor\->get(\-universal_name => \*(Aqtf1\*(Aq);
\&  my $map1 = Bio::Map::GeneMap\->get(\-universal_name => "BRCA2",
\&                                    \-species => "human");
\&  my $map2 = Bio::Map::GeneMap\->get(\-universal_name => "BRCA2",
\&                                    \-species => "mouse");
\&  Bio::Map::Position\->new(\-map => $map1,
\&                          \-element => $tf,
\&                          \-start => \-500,
\&                          \-length => 10);
\&  Bio::Map::Position\->new(\-map => $map2,
\&                          \-element => $tf,
\&                          \-start => \-250,
\&                          \-length => 10);
\&
\&  # Find out where the transcription factor binds
\&  foreach $pos ($tf\->get_positions) {
\&    print $tf\->universal_name, " binds at position " $pos\->value, " relative to ",
\&          $pos\->relative\->description, " of gene ",
\&          $pos\->map\->universal_name, " in species ", $pos\->map\->species, "\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A transcription factor modelled as a mappable element. It can have multiple
binding sites (positions) near multiple genes (maps).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 8
\& Title   : new
\& Usage   : my $tf = Bio::Map::TranscriptionFactor\->new();
\& Function: Builds a new Bio::Map::TranscriptionFactor object
\& Returns : Bio::Map::TranscriptionFactor
\& Args    : \-universal_name => string name of the TF (in a form common to all
\&                              species that have the TF, but unique amongst
\&                              non\-orthologous TFs), REQUIRED
\&           \-description    => string, free text description of the TF
.Ve
.SS "get"
.IX Subsection "get"
.Vb 9
\& Title   : get
\& Usage   : my $obj = Bio::Map::TranscriptionFactor\->get();
\& Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or
\&           gets a pre\-existing one that shares the same universal_name.
\& Returns : Bio::Map::TranscriptionFactor
\& Args    : \-universal_name => string name of the TF (in a form common to all
\&                              species that have the TF, but unique amongst
\&                              non\-orthologous TFs), REQUIRED
\&           \-description    => string, free text description of the TF
.Ve
.SS "universal_name"
.IX Subsection "universal_name"
.Vb 7
\& Title   : universal_name
\& Usage   : my $name = $obj\->universal_name
\& Function: Get/Set TF name, corresponding to the name of the TF in a form shared
\&           by orthologous versions of the TF in different species, but otherwise
\&           unique.
\& Returns : string
\& Args    : none to get, OR string to set
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& Title   : description
\& Usage   : my $desc = $obj\->description
\& Function: Get/Set a description of the TF.
\& Returns : string
\& Args    : none to get, OR string to set
.Ve