ENCODEBindingConsensus-class {ENCODExplorer} | R Documentation

## ENCODEBindingConsensus: consensus peaks derived from ENCODE files.

### Description

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.

### Usage

    ## 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)

### Arguments

`x` | The ENCODESummary object.
`value` | The new names for the elements of the ENCODESummary object.
`object` | The ENCODESummary object.

### Value

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.

### Slots

`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.

### Methods

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.

### Examples

      res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")
      peaks(res)
      consensus(res)

[Package ENCODExplorer version 2.13.1 Index]