reducedDims: Methods for Reduced Dimensions in ExperimentSubset objects

In ExperimentSubset: Manages subsets of data with Bioconductor Experiment 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")

ExperimentSubset documentation built on Nov. 8, 2020, 5:03 p.m.