Grey Lists - Mask Artefact Regions Based on ChIP Inputs

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Documentation for package ‘GreyListChIP’ version 1.41.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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