Grey Lists - Mask Artefact Regions Based on ChIP Inputs


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Documentation for package ‘GreyListChIP’ version 1.18.0

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calcThreshold Calculate Read Count Threshold
calcThreshold-method Calculate Read Count Threshold
ce10.blacklist A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
countReads Count reads from a 'BamFile'
countReads-method Count reads from a 'BamFile'
dm3.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
export-method '"GreyList"' Objects
getKaryotype Replace the karyotype of a 'GreyList' object
getKaryotype-method Replace the karyotype of a 'GreyList' object
gl A sample 'GreyList' object for use in examples.
grch37.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
grch38.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
GreyList '"GreyList"' Objects
greyList A sample 'GreyList' object for use in examples.
GreyList-class '"GreyList"' Objects
greyListBS Construct a grey list with default arguments
hg19.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
hg38.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
initialize-method '"GreyList"' Objects
loadKaryotype Load a karyotype from a file
loadKaryotype-method Load a karyotype from a file
makeGreyList Generate a grey list from a 'GreyList' object
makeGreyList-method Generate a grey list from a 'GreyList' object
mm10.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
mm9.blacklist 'GRanges' objects representing ENCODE signal artefact or "black list" regions.
setRegions Replace the set of regions of a 'GreyList' object
setRegions-method Replace the set of regions of a 'GreyList' object
show-method '"GreyList"' Objects