reducedDims {ExperimentSubset}R Documentation

Methods for Reduced Dimensions in ExperimentSubset objects

Description

A wrapper to the reducedDims method with additional support for subsets.

Usage

reducedDims(object, withDimnames, subsetName)

## S4 method for signature 'ANY'
reducedDims(object, withDimnames, subsetName)

Arguments

object

ExperimentSubset Input ExperimentSubset object or any object supported by reducedDims method.

withDimnames

logical(1) Same as withDimnames in reducedDims method.

subsetName

character(1) Specify the name of the subset from which the reducedDims should be fetched from. If missing, reducedDims method is called on the main object.

Value

The reducedDims from the specified subset or same as link[SingleCellExperiment]reducedDims when subsetName is missing.

Examples

data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(1:1500), cols = c(1:1500),
parentAssay = "counts")
reducedDim(es, type = "PCA_1",
subsetName = "subset1") <- scater::calculatePCA(
assay(es, "subset1"))
reducedDim(es, type = "PCA_2",
subsetName = "subset1") <- scater::calculatePCA(
assay(es, "subset1"))
reducedDims(es, subsetName = "subset1")

[Package ExperimentSubset version 1.0.0 Index]