seuratICA: seuratICA Computes ICA on the input sce object and stores the...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

seuratICA Computes ICA on the input sce object and stores the calculated independent components within the sce object

Usage

seuratICA(inSCE, useAssay, reducedDimName = "seuratICA", nics = 20)

Arguments

inSCE	(sce) object on which to compute ICA
useAssay	Assay containing scaled counts to use in ICA.
reducedDimName	Name of new reducedDims object containing Seurat ICA Default seuratICA.
nics	Number of independent components to compute. Default 20.

Value

Updated SingleCellExperiment object which now contains the computed independent components

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- seuratNormalizeData(sce, useAssay = "counts")
sce <- seuratFindHVG(sce, useAssay = "counts")
sce <- seuratScaleData(sce, useAssay = "counts")
sce <- seuratICA(sce, useAssay = "counts")

## End(Not run)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.