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 |