queryConsensusPeaks: Queries ENCODE for consensus peaks.

In CharlesJB/ENCODExplorer: A compilation of ENCODE metadata

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")

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