ce10.blacklist {GreyListChIP}R Documentation

A GRanges object representing ENCODE signal artefact or "black list" regions.

Description

These objects are made from the so-called black list or signal artefact regions defined by Anshul Kundaje Alan Boyle as part of the ENCODE and modENCODE projects. They are regions which show a signal in essentially any ChIP or similar experiment. For this reason it is useful to remove reads aligning to these regions before carrying out any sort of functional genomics analysis.

These objects can be merged with GreyList objects to perform grey list and black list filtering in one step. They are included in the package as a convenience, with the permission of the creators.

Usage

ce10.blacklist

Format

An S4 GRanges object.

Value

GRanges objects defining the black list regions.

Source

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. https://sites.google.com/site/anshulkundaje/projects/blacklists


[Package GreyListChIP version 1.16.0 Index]