runSeuratScaleData Scales the input sce object according to the input parameters

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")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
}