NAME

Bio::ViennaNGS::BamStatSummary - Moose interface to analyze, summarize and compare BAM mapping statistics data structure produced by Bio::ViennaNGS::BamStat

SYNOPSIS

use Bio::ViennaNGS::BamStatSummary;

$bamsummary->populate_data();
$bamsummary->populate_countStat();
$bamsummary->dump_countStat("csv");
$bamsummary->make_BarPlot();

$bamsummary->make_BoxPlot("data_edit" ) if( $bamsummary->has_control_edit   );
$bamsummary->make_BoxPlot("data_clip" ) if( $bamsummary->has_control_clip   );
$bamsummary->make_BoxPlot("data_match") if( $$bamsummary->has_control_match );
$bamsummary->make_BoxPlot("data_qual" ) if( $bamsummary->has_control_qual   );

DESCRIPTION

This module provides a Moose interface to process the mapping statistics of single BAM file. It uses the data structure as produced by Bio::ViennaNGS::BamStat, summarizes the data and compares different BAM files. Output is written both as CSV files and graphical representation of the results. Internally, this modules build on Statistics::R.

DEPENDENCIES

Statistics::R

Path::Class

Tie::Hash::Indexed

Moose

SEE ALSO

Bio::ViennaNGS

Bio::ViennaNGS::BamStat

AUTHORS

Fabian Amman <fabian@tbi.univie.ac.at>

Michael T. Wolfinger <michael@wolfinger.eu>

COPYRIGHT AND LICENSE

Copyright (C) 2015 by Michael T. Wolfinger

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.