| Bio::Map::TranscriptionFactor(3pm) | User Contributed Perl Documentation | Bio::Map::TranscriptionFactor(3pm) |
Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable element
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 => 'tf1');
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, "\n";
}
A transcription factor modelled as a mappable element. It can have multiple binding sites (positions) near multiple genes (maps).
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
| 2018-10-27 | perl v5.26.2 |