ENCODEExpressionSummary-class {ENCODExplorer} | R Documentation

## ENCODEExpressionSummary summarize means of expression across ENCODE files.

### Description

ENCODEExpressionSummary objects represent means (or medians) of expression levels across multiple replicate samples, split by arbitrary metadata columns. They can be constructed using the queryGeneExpression, queryTranscriptExpression and buildExpressionSummary functions.

### Usage

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

    metric_data(x)

    ## S4 method for signature 'ENCODEExpressionSummary'
    metric_data(x)

    metric(x)

    ## S4 method for signature 'ENCODEExpressionSummary'
    metric(x)

    raw_data(x)

    ## S4 method for signature 'ENCODEExpressionSummary'
    raw_data(x)

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

### Arguments

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

### Value

For `raw_data`, a `list` of GRangesList of the per-condition original expression tables used to build the object. For `metric`, the regular expression used to select the column of metric values from the ENCODE files. For `metric_data`, a data.frame of the per-condition metric values.

### Slots

`raw_data`

  A list of data-frames containing the full raw data of each of the downloaded ENCODE files.

`metric`

  A character giving the regular expression used to extract expression metrics from the ENCODE files.

`metric_data`

  A data.frame of the per-condition metric values.

`expression_type`

  The type of expression which is being reported, either gene or transcripts.

### Methods

ENCODEExpressionSummary object can be accessed through the methods from the ENCODESummary class, as well as ENCODEBindingConsensus-specific methods:

`raw_data`

  Returns a `list` of GRangesList of the per-condition original expression tables used to build the object.

`metric`

  Returns the regular expression used to select the column of metric values from the ENCODE files.

`metric_data`

  Returns a data.frame of the per-condition metric values.

### Examples

      res = queryGeneExpression("bone marrow")
      raw_data(res)
      metric(res)
      metric_data(res)

[Package ENCODExplorer version 2.12.1 Index]