queryConsensusPeaks {ENCODExplorer} | R Documentation |
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.
queryConsensusPeaks( biosample_name, assembly, target, simplify = FALSE, use_interactive = FALSE )
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. |
If you wish to have more control over the files used to build the consensus,
use buildConsensusPeaks
.
An object of class ENCODEBindingConsensus.
queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")