runSeuratScaleData: runSeuratScaleData Scales the input sce object according to...

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

runSeuratScaleData Scales the input sce object according to the input parameters

Description

runSeuratScaleData Scales the input sce object according to the input parameters

Usage

runSeuratScaleData(
  inSCE,
  useAssay = "seuratNormData",
  scaledAssayName = "seuratScaledData",
  model = "linear",
  scale = TRUE,
  center = TRUE,
  scaleMax = 10,
  verbose = TRUE
)

Arguments

inSCE	(sce) object to scale
useAssay	Assay containing normalized counts to scale.
scaledAssayName	Name of new assay containing scaled data. Default seuratScaledData.
model	selected model to use for scaling data. Default "linear".
scale	boolean if data should be scaled or not. Default TRUE.
center	boolean if data should be centered or not. Default TRUE
scaleMax	maximum numeric value to return for scaled data. Default 10.
verbose	Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

Scaled SingleCellExperiment object

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")

## End(Not run)

compbiomed/singleCellTK documentation built on June 11, 2025, 9:45 a.m.