Description Usage Arguments Value Slots Methods Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## 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.
1 2 3 | res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")
peaks(res)
consensus(res)
|
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