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

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

runSeuratICA(
  inSCE,
  useAssay,
  reducedDimName = "seuratICA",
  features = NULL,
  nics = 20,
  seed = NULL
)

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.

features

Specify the feature names or rownames which should be used for computation of ICA. Default is NULL which will use the previously stored variable features.

nics

Number of independent components to compute. Default 20.

seed

Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.

Value

Updated SingleCellExperiment object which now contains the computed independent components

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratICA(sce, useAssay = "counts")
}