ENCODESummary-class {ENCODExplorer} | R Documentation

## ENCODESummary objects: summaries of multiple ENCODE files.

### Description

ENCODESummary objects is the base class of ENCODEBindingConsensus-class and ENCODEExpressionSummary-class objects. It provides methods to query which files were used to build the summary, the names of the grouped elements as well as their metadata.

### Usage

    ## S4 method for signature 'ENCODESummary'
    names(x)

    ## S4 replacement method for signature 'ENCODESummary,character'
    names(x) <- value

    ## S4 method for signature 'ENCODESummary'
    length(x)

    ## S4 method for signature 'ENCODESummary'
    metadata(x)

    file_metadata(x)

    ## S4 method for signature 'ENCODESummary'
    file_metadata(x)

    files(x)

    ## S4 method for signature 'ENCODESummary'
    files(x)

    ## S4 method for signature 'ENCODESummary'
    show(object)

### Arguments

`x` | The ENCODESummary object.
`value` | The new names for the elements of the ENCODESummary object.
`object` | The ENCODESummary object.

### Value

For `names`, `names<-`, a copy of the object. For `length`, the number of elements. For `files`, a character vector. For `file_metadata`, a list of data-frames with each file's metadata. For `metadata`, a data-frame with the discriminating metadata of each sample group.

### Slots

`files`

  The path of the files used in this summary.

`file_metadata`

  A list of data-frames representing the ENCODE metadata of the files used to build the per-condition consensus.

`metadata`

  A data-frame with the metadata of each element in the summary.

### Methods

ENCODESummary object can be accessed through a variety of methods:

`names`

  Returns the names of the elements.

`names<-`

  Sets the names of the elements.

`length`

  Returns the number of elements.

`files`

  Returns a character vector of the ENCODE files used to build this object.

`file_metadata`

  Returns a list of per-condition metadata of the ENCODE files used to build the object.

`metadata`

  Returns a data-frame of the common per-condition metadata of the ENCODE files used to build the object.

`show`

  Print a summary of the object.

### Examples

      res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")
      names(res)
      files(res)
      metadata(res)
      print(res)

[Package ENCODExplorer version 2.14.0 Index]