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

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)