ENCODEExpressionSummary-class {ENCODExplorer} | R Documentation |
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.
## 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)
x |
The ENCODESummary object. |
value |
The new names for the elements of the ENCODESummary object. |
object |
The ENCODESummary object. |
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.
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.
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.
res = queryGeneExpression("bone marrow") raw_data(res) metric(res) metric_data(res)