NAME

diffReps::SlideWindow - class to deal with a sliding window. diffReps::ChromaModSite - class to deal with chromatin modification site, inherited from SlideWindow. diffReps::RegionList - class for a list of modification regions.

SYNOPSIS

  slideWindow = new diffReps::SlideWindow;
  site = new diffReps::ChromaModSite;
  regList = new diffReps::RegionList;

DESCRIPTION

In order to perform differential analysis for ChIP-seq data, we need to define classes and methods that can retrieve short read counts for a designated window; perform statistics and book-keep important information.

EXPORT

None by default.

SEE ALSO

MyShortRead::SRBed

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AUTHOR

Li Shen, <li.shen@mssm.edu>

COPYRIGHT AND LICENSE

Copyright (C) 2011 by Li Shen

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.8 or, at your option, any later version of Perl 5 you may have available.