Grey Lists - Mask Artefact Regions Based on ChIP Inputs


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Documentation for package ‘GreyListChIP’ version 1.40.0

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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.
ce11.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 A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
dm6.blacklist A 'GRanges' object 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
grch37.blacklist A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
grch38.blacklist A 'GRanges' object 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 A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
hg38.blacklist A 'GRanges' object 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 A 'GRanges' object representing ENCODE signal artefact or "black list" regions.
mm9.blacklist A 'GRanges' object 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