RangedRaggedAssay-class {MultiAssayExperiment} | R Documentation |
An extension of the GRangesList class (DEFUNCT)
Subsetting a RangedRaggedAssay can be done using either rownames and column names
## S4 method for signature 'RangedRaggedAssay,ANY,ANY,ANY' x[i, j, ..., drop = TRUE] ## S4 method for signature 'RangedRaggedAssay,GRanges,ANY,ANY' x[i, j, ..., drop = TRUE] ## S4 method for signature 'RangedRaggedAssay' dim(x) ## S4 method for signature 'RangedRaggedAssay' dimnames(x) ## S4 replacement method for signature 'RangedRaggedAssay,list' dimnames(x) <- value ## S4 method for signature 'RangedRaggedAssay' disjoin(x, mcolname = NULL, simplify = BiocGenerics::mean, ...) ## S4 method for signature 'RangedRaggedAssay' show(object) ## S4 method for signature 'RangedRaggedAssay' longFormat(object, ...) ## S4 method for signature 'RangedRaggedAssay' mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, mcolname = NULL, ...)
x |
A |
i |
Either a |
j |
Either a |
... |
Additional arguments. See details for more information. |
drop |
logical (default TRUE) whether to drop empty columns |
value |
A |
mcolname |
A single character string indicating metadata column to use for summaries |
simplify |
A function for combining duplicate measurements (e.g., mean) |
object |
A |
replicates |
mergeReplicates: A |
The ...
argument allows the user to specify arguments in the
subsetByOverlaps
function. When calling the
mergeReplicates
method, the additional arguments correspond to those
in either the assay
method or the mergeReplicates
method.
The mergeReplicates
arguments include a function for applying over
the rows (combine
) and a vectorized
argument which indicates
whether the given function is vectorized or not.
A RangedRaggedAssay
class object
[
: Subset a RangedRaggedAssay
with either
chracter
, numeric
, or logical
[
: Subset a RangedRaggedAssay
using a
GRanges
class object
dim
: Obtain dimension lengths of a
RangedRaggedAssay
class object
dimnames
: Get dimension names
for a RangedRaggedAssay
dimnames<-
: value: A modified RangedRaggedAssay
object
disjoin
: Separate non-disjoint ranges and merge
with function
show
: show method for
the RangedRaggedAssay
class
longFormat
: RangedRaggedAssay class method
to return a DataFrame of selected “mcolname” column, defaults to score
mergeReplicates
: (deprecated) Use metadata column to produce
a matrix which can then be merged across replicates.
assay,RangedRaggedAssay,missing-method