MultiAssayExperiment-methods {MultiAssayExperiment} | R Documentation |
A set of accessor and setter generic functions to extract
either the sampleMap
, the ExperimentList
,
colData
, or metadata
slots of a
MultiAssayExperiment
object
## S4 method for signature 'MultiAssayExperiment' sampleMap(x) ## S4 method for signature 'MultiAssayExperiment' experiments(x) ## S4 method for signature 'MultiAssayExperiment' colData(x, ...) ## S4 method for signature 'MultiAssayExperiment' metadata(x) ## S4 replacement method for signature 'MultiAssayExperiment,DataFrame' sampleMap(object) <- value ## S4 replacement method for signature 'MultiAssayExperiment,ANY' sampleMap(object) <- value ## S4 replacement method for signature 'MultiAssayExperiment,ExperimentList' experiments(object) <- value ## S4 replacement method for signature 'MultiAssayExperiment,DataFrame' colData(x) <- value ## S4 replacement method for signature 'MultiAssayExperiment,ANY' colData(x) <- value ## S4 replacement method for signature 'MultiAssayExperiment' metadata(x, ...) <- value ## S4 replacement method for signature 'MultiAssayExperiment' x$name <- value ## S4 replacement method for signature 'MultiAssayExperiment' names(x) <- value ## S4 method for signature 'MultiAssayExperiment' x$name
... |
Argument not in use |
object, x |
A |
value |
See details. |
name |
A column in |
Accessors: Either a sampleMap
, ExperimentList
, or
DataFrame
object
Setters: A MultiAssayExperiment
object
Eponymous names for accessing MultiAssayExperiment
slots with the
exception of the ExperimentList accessor named experiments
.
colData: Access the colData
slot
sampleMap: Access the sampleMap
slot
experiments: Access the ExperimentList slot
'[[': Access the ExperimentList slot
'$': Access a column in colData
Setter method values (i.e., 'function(x) <- value
'):
experiments<-: An ExperimentList
object
containing experiment data of supported classes
sampleMap<-: A DataFrame
object relating
samples to biological units and assays
colData<-: A DataFrame
object describing the
biological units
metadata<-: A list
object of metadata
'[[<-': Equivalent to the experiments<-
setter method for
convenience
'$<-': A vector to replace the indicated column in colData
## Load example MultiAssayExperiment example(MultiAssayExperiment) ## Access the sampleMap sampleMap(mae) ## Replacement method for a MultiAssayExperiment sampleMap sampleMap(mae) <- S4Vectors::DataFrame() ## Access the ExperimentList experiments(mae) ## Replace with an empty ExperimentList experiments(mae) <- ExperimentList() ## Access the metadata metadata(mae) ## Replace metadata with a list metadata(mae) <- list(runDate = format(Sys.time(), "%B %d, %Y")) ## Access the colData colData(mae) ## Access a column in colData mae$age ## Replace a column in colData mae$age <- mae$age + 1