ENCODESummary-class: ENCODESummary objects: summaries of multiple ENCODE files.

In CharlesJB/ENCODExplorer: A compilation of ENCODE metadata

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)

CharlesJB/ENCODExplorer documentation built on Dec. 9, 2019, 10:11 a.m.