queryConsensusPeaks {ENCODExplorer} | R Documentation

## Queries ENCODE for consensus peaks.

### Description

Queries the ENCODE metadata to determine which peak files exists for the `target` protein in the `biosample_name` biosample for the `assembly` genomic assembly, then builds per-condition (as determined by the `treatment` column and its adjuncts) consensus peaks.

### Usage

    queryConsensusPeaks(
      biosample_name,
      assembly,
      target,
      simplify = FALSE,
      use_interactive = FALSE
    )

### Arguments

`biosample_name` | The cell-line/tissue for which consensus peaks should be queried.
`assembly` | The target genomic assembly.
`target` | The target protein.
`simplify` | If TRUE, non-discriminatory columns are removed from the metadata, and if only one sample group is found, it is renamed "All".
`use_interactive` | If TRUE, the user will be prompted when ENCODExplorer must choose how to filter the available data.

### Details

If you wish to have more control over the files used to build the consensus, use `buildConsensusPeaks`.

### Value

An object of class ENCODEBindingConsensus.

### See Also

`buildConsensusPeaks`

### Examples

      queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")

[Package ENCODExplorer version 2.13.1 Index]