Description Getters Single-result setter Other setters Author(s) Examples

Methods to get or set dimensionality reduction results in a SingleCellExperiment object. These are typically used to store and retrieve low-dimensional representations of single-cell datasets. Each row of a reduced dimension result is expected to correspond to a column of the SingleCellExperiment object.

In the following examples, `x`

is a SingleCellExperiment object.

`reducedDim(x, type, withDimnames=TRUE)`

:-
Retrieves a matrix (or matrix-like object) containing reduced dimension coordinates for cells (rows) and dimensions (columns).

`type`

is either a string specifying the name of the dimensionality reduction result in`x`

to retrieve, or a numeric scalar specifying the index of the desired result. If`withDimnames=TRUE`

, row names of the output matrix are replaced with the column names of`x`

. `reducedDimNames(x)`

:-
Returns a character vector containing the names of all dimensionality reduction results in

`x`

. This is guaranteed to be of the same length as the number of results, though the names may not be unique. `reducedDims(x, withDimnames=TRUE)`

:-
Returns a named List of matrices containing one or more dimensionality reduction results. Each result is a matrix (or matrix-like object) with the same number of rows. If

`withDimnames=TRUE`

, row names of each matrix are replaced with the column names of`x`

.

`reducedDim(x, type) <- value`

will add or replace a dimensionality reduction result
in a SingleCellExperiment object `x`

.
The value of `type`

determines how the result is added or replaced:

If

`type`

is missing,`value`

is assigned to the first result. If the result already exists, its name is preserved; otherwise it is given a default name`"unnamed1"`

.If

`type`

is a numeric scalar, it must be within the range of existing results, and`value`

will be assigned to the result at that index.If

`type`

is a string and a result exists with this name,`value`

is assigned to to that result. Otherwise a new result with this name is append to the existing list of results.

`value`

is expected to be a matrix or matrix-like object with number of rows equal to `ncol(x)`

.
Alternatively, if `value`

is `NULL`

, the result corresponding to `type`

is removed from the object.

In the following examples, `x`

is a SingleCellExperiment object.

`reducedDims(x) <- value`

:-
Replaces all dimensionality reduction results in

`x`

with those in`value`

. The latter should be a list-like object containing any number of matrices or matrix-like objects with number of rows equal to`ncol(x)`

.If

`value`

is named, those names will be used to name the dimensionality reduction results in`x`

. Otherwise, unnamed results are assigned default names prefixed with`"unnamed"`

.If

`value`

is`NULL`

, all dimensionality reduction results in`x`

are removed. `reducedDimNames(x) <- value`

:-
Replaces all names for dimensionality reduction results in

`x`

with a character vector`value`

. This should be of length equal to the number of results currently in`x`

.

Aaron Lun and Kevin Rue-Albrecht

1 2 3 4 5 6 7 8 9 10 | ```
example(SingleCellExperiment, echo=FALSE)
reducedDim(sce, "PCA")
reducedDim(sce, "tSNE")
reducedDims(sce)
reducedDim(sce, "PCA") <- NULL
reducedDims(sce)
reducedDims(sce) <- SimpleList()
reducedDims(sce)
``` |

SingleCellExperiment documentation built on Nov. 8, 2020, 7:51 p.m.

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