runSeuratNormalizeData: runSeuratNormalizeData Wrapper for NormalizeData() function...

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

runSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters

Description

runSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters

Usage

runSeuratNormalizeData(
  inSCE,
  useAssay,
  normAssayName = "seuratNormData",
  normalizationMethod = "LogNormalize",
  scaleFactor = 10000,
  verbose = TRUE
)

Arguments

inSCE	(sce) object to normalize
useAssay	Assay containing raw counts to use for normalization.
normAssayName	Name of new assay containing normalized data. Default seuratNormData.
normalizationMethod	selected normalization method. Default "LogNormalize".
scaleFactor	numeric value that represents the scaling factor. Default 10000.
verbose	Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

Normalized SingleCellExperiment object

Examples

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

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.