buildConsensusPeaks {ENCODExplorer} | R Documentation

## Calculates the consensus peaks defined by the results of a previously completed ENCODE query.

### Description

This function takes the result of a previous call to `queryEncode`, splits the contained peak files by conditions (as specified by the `split_by` argument), then builds consensus peaks for each condition.

### Usage

    buildConsensusPeaks(
      query_results,
      split_by = NULL,
      consensus_threshold = 1,
      simplify = FALSE,
      temp_dir = ".",
      force = FALSE,
      consensus_threshold_n = NULL
    )

### Arguments

`query_results` | A data.table returned by `queryEncode` or `queryEncodeGeneric`.
`split_by` | A vector of column names from query_results that will be used to split the consensus binding sites according to condition. If `NULL`, all elements of query_results are used in the same consensus calculation.
`consensus_threshold` | A numeric value between 0 and 1, indicating the proportion of peak files in which a peak must appear for it to be included within the consensus.
`simplify` | If TRUE, non-discriminatory columns are removed from the metadata, and if only one sample group is found, it is renamed "All".
`temp_dir` | The path to a directory where peak files will be downloaded.
`force` | A logical indicating whether already present files be redownloaded.
`consensus_threshold_n` | An integer indicating the number of peak files in which a peak must appear for it to be included within the consensus. IF this argument is provided, it supercedes consensus_threshold.

### Value

An object of class ENCODEBindingConsensus.

### Examples

    query_results = queryEncodeGeneric(biosample_name="A549", assembly="GRCh38",
                                      file_format="^bed$", output_type="^peaks$",
                                      treatment_duration_unit="minute",
                                      treatment_duration="(^5$|^10$)",
                                      target="NR3C1", fixed=FALSE)
    res = buildConsensusPeaks(query_results, split_by=c("treatment_duration"),
                              consensus_threshold=0.5)

[Package ENCODExplorer version 2.13.1 Index]