ENCODEBindingConsensus-class: ENCODEBindingConsensus: consensus peaks derived from ENCODE...

In CharlesJB/ENCODExplorer: A compilation of ENCODE metadata

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)

CharlesJB/ENCODExplorer documentation built on Dec. 9, 2019, 10:11 a.m.