reducedDimension: Reduced dimension representation for cells in an SCESet...

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

SCESet objects can contain a matrix of reduced dimension coordinates for cells. These functions conveniently access and replace the reduced dimension coordinates with the value supplied, which must be a matrix of the correct size. The function redDim is simply shorthand for reducedDimension.

Usage

reducedDimension(object)

reducedDimension(object) <- value

redDim(object)

redDim(object) <- value

reducedDimension.SCESet(object)

## S4 method for signature 'SCESet'
reducedDimension(object)

redDim.SCESet(object)

## S4 method for signature 'SCESet'
redDim(object)

## S4 replacement method for signature 'SCESet,matrix'
reducedDimension(object) <- value

## S4 replacement method for signature 'SCESet,matrix'
redDim(object) <- value

Arguments

object	a SCESet object.
value	a matrix of class "numeric" containing reduced dimension coordinates for cells.

Value

If accessing the reducedDimension slot, then the matrix of reduced dimension coordinates. If replacing the reducedDimension slot then the new matrix is added to the SCESet object.

Author(s)

Davis McCarthy

Examples

data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
reducedDimension(example_sceset)

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.