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.\" ========================================================================
.\"
.IX Title "Bio::Variation::DNAMutation 3pm"
.TH Bio::Variation::DNAMutation 3pm "2021-03-04" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Variation::DNAMutation \- DNA level mutation class
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&    $dnamut = Bio::Variation::DNAMutation\->new
\&        (\*(Aq\-start\*(Aq         => $start,
\&         \*(Aq\-end\*(Aq           => $end,
\&         \*(Aq\-length\*(Aq        => $len,
\&         \*(Aq\-upStreamSeq\*(Aq   => $upflank,
\&         \*(Aq\-dnStreamSeq\*(Aq   => $dnflank,
\&         \*(Aq\-proof\*(Aq         => $proof,
\&         \*(Aq\-isMutation\*(Aq    => 1,
\&         \*(Aq\-mut_number\*(Aq    => $mut_number
\&        );
\&    $a1 = Bio::Variation::Allele\->new;
\&    $a1\->seq(\*(Aqa\*(Aq);
\&    $dnamut\->allele_ori($a1);
\&    my $a2 = Bio::Variation::Allele\->new;
\&    $a2\->seq(\*(Aqt\*(Aq);
\&    $dnamut\->add_Allele($a2);
\&
\&    print "Restriction changes are ", $dnamut\->restriction_changes, "\en";
\&
\&    # add it to a SeqDiff container object
\&    $seqdiff\->add_Variant($dnamut);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The instantiable class Bio::Variation::DNAMutation describes basic
sequence changes in genomic \s-1DNA\s0 level. It uses methods defined in
superclass Bio::Variation::VariantI. See Bio::Variation::VariantI
for details.
.PP
If the variation described by a DNAMutation object is transcibed, link
the corresponding Bio::Variation::RNAChange object to it using
method \fBRNAChange()\fR. See Bio::Variation::RNAChange for more information.
.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 lists  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
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 \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "CpG"
.IX Subsection "CpG"
.Vb 7
\& Title   : CpG
\& Usage   : $obj\->CpG()
\& Function: sets and returns boolean values for variation
\&           hitting a CpG site.  Unset value return \-1.
\& Example : $obj\->CpG()
\& Returns : boolean
\& Args    : optional true of false value
.Ve
.SS "RNAChange"
.IX Subsection "RNAChange"
.Vb 6
\& Title   : RNAChange
\& Usage   : $mutobj = $obj\->RNAChange;
\&         : $mutobj = $obj\->RNAChange($objref);
\& Function: Returns or sets the link\-reference to a mutation/change object.
\&           If there is no link, it will return undef
\& Returns : an obj_ref or undef
.Ve
.SS "label"
.IX Subsection "label"
.Vb 3
\& Title   : label
\& Usage   : $obj\->label();
\& Function:
\&
\&            Sets and returns mutation event label(s).  If value is not
\&            set, or no argument is given returns false.  Each
\&            instantiable subclass of L<Bio::Variation::VariantI> needs
\&            to implement this method. Valid values are listed in
\&            \*(AqMutation event controlled vocabulary\*(Aq in
\&            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
\&
\& Example :
\& Returns : string
\& Args    : string
.Ve
.SS "sysname"
.IX Subsection "sysname"
.Vb 3
\& Title   : sysname
\& Usage   : $self\->sysname
\& Function:
\&
\&           This subroutine creates a string corresponding to the
\&           \*(Aqsystematic name\*(Aq of the mutation. Systematic name is
\&           specified in Antonorakis & MDI Nomenclature Working Group:
\&           Human Mutation 11:1\-3, 1998.
\&
\& Returns : string
.Ve