ENCODESummary-class {ENCODExplorer} | R Documentation |
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.
## 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)
x |
The ENCODESummary object. |
value |
The new names for the elements of the ENCODESummary object. |
object |
The ENCODESummary object. |
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.
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.
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.
res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF") names(res) files(res) metadata(res) print(res)