R/ExperimentList-class.R
, R/MultiAssayExperiment-methods.R
, R/MultiAssayExperiment-helpers.R
, and 1 more
ExperimentList-class.Rd
The ExperimentList
class is a container that builds on
the SimpleList
with additional checks for consistency in experiment
names and length. It contains a SimpleList
of experiments with
sample identifiers. One element present per experiment performed.
Convert from SimpleList
or list
to the multi-experiment data
container. When using the mergeReplicates method, additional
arguments are passed to the given simplify
function argument (e.g.,
na.rm = TRUE
)
# S4 method for ExperimentList
show(object)
# S4 method for ExperimentList
isEmpty(x)
# S4 method for ExperimentList
dimnames(x)
# S4 method for ExperimentList
colnames(x, do.NULL = TRUE, prefix = "col")
# S4 method for ExperimentList
rownames(x, do.NULL = TRUE, prefix = "row")
# S4 method for ExperimentList
mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...)
# S4 method for ANY,missing
assay(x, i, withDimnames = TRUE, ...)
# S4 method for ExperimentList
assays(x, withDimnames = TRUE, ...)
# S4 method for ExperimentList,missing
assay(x, i, withDimnames = TRUE, ...)
# S4 method for ExperimentList,numeric
assay(x, i, withDimnames = TRUE, ...)
# S4 method for ExperimentList,character
assay(x, i, withDimnames = TRUE, ...)
An ExperimentList
object
See ?base::rownames
for a description of
these arguments.
mergeReplicates: A list
or LogicalList
where each element represents a sample and a vector of repeated measurements
for the sample
A function for merging columns where duplicates are indicated by replicates
Additional arguments. See details for more information.
A scalar character
or integer
index
logical (default TRUE) whether to return dimension names
An ExperimentList
class object
show(ExperimentList)
: Show method for
ExperimentList
class
isEmpty(ExperimentList)
: check for zero length across all
experiments
dimnames(ExperimentList)
: Get the dimension names for
an ExperimentList
using CharacterList
colnames(ExperimentList)
: Get the column names for an ExperimentList
as a CharacterList
slightly more efficiently
rownames(ExperimentList)
: Get the row names for an ExperimentList
as a CharacterList
slightly more efficiently
mergeReplicates(ExperimentList)
: Apply the mergeReplicates method on the
ExperimentList elements
assay(x = ANY, i = missing)
: Obtain the specified assay with a numeric
or character
reference
assays(ExperimentList)
: Get the assay data from each element in the
ExperimentList
Convert a list
or S4 List
to an ExperimentList using the
as()
function.
In the following example, x
is either a list
or
List:
\code{as(x, "ExperimentList")}
ExperimentList()
#> ExperimentList class object of length 0:
#>