ENCODEBindingConsensus-class {ENCODExplorer} | R Documentation |
ENCODEBindingConsensus objects represent the intersection of called peaks across multiple replicates, split by arbitrary metadata columns. They can be constructed using the queryConsensusPeaks and buildConsensusPeaks functions.
## S4 replacement method for signature 'ENCODEBindingConsensus,character' names(x) <- value peaks(x) ## S4 method for signature 'ENCODEBindingConsensus' peaks(x) consensus(x) ## S4 method for signature 'ENCODEBindingConsensus' consensus(x) ## S4 method for signature 'ENCODEBindingConsensus' show(object)
x |
The ENCODESummary object. |
value |
The new names for the elements of the ENCODESummary object. |
object |
The ENCODESummary object. |
For peaks
, a list
of GRangesList of the
per-condition original peaks used to build the object. For
consensus
, a GRangesList of the per-condition
consensus peaks.
peaks
The per-condition original peaks used to build the consensus.
consensus
The per-condition consensus peaks.
consensus_threshold
The proportion of replicates which must bear a specific peak for it to be added to the set of consensus peaks.
ENCODEBindingConsensus object can be accessed through the methods from the ENCODESummary class, as well as ENCODEBindingConsensus-specific methods:
peaks
Returns a list
of GRangesList
of the per-condition original peaks used to build
the object.
consensus
Returns a GRangesList of the per-condition consensus peaks.
res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF") peaks(res) consensus(res)