R: Grey Lists - Mask Artefact Regions Based on ChIP Inputs

# Grey Lists - Mask Artefact Regions Based on ChIP Inputs

## Documentation for package ‘GreyListChIP’ version 1.44.0

- 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