LogNormalizeUsingAlternateAssay: LogNormalizeUsingAlternateAssay

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

LogNormalizeUsingAlternateAssay

Description

LogNormalizeUsingAlternateAssay

Usage

LogNormalizeUsingAlternateAssay(
  seuratObj,
  assayToNormalize,
  assayForLibrarySize = "RNA",
  scale.factor = 10000,
  maxLibrarySizeRatio = 0.01
)

Arguments

seuratObj	The seurat object
assayToNormalize	The name of the assay to normalize
assayForLibrarySize	The name of the assay from which to derive library sizes. This will be added to the library size of assayToNormalize.
scale.factor	A scale factor to be applied in normalization
maxLibrarySizeRatio	This normalization relies on the assumption that the library size of the assay being normalized in negligible relative to the assayForLibrarySize. To verify this holds true, the method will error if librarySize(assayToNormalize)/librarySize(assayForLibrarySize) exceeds this value

bimberlabinternal/CellMembrane documentation built on Nov. 15, 2024, 9:34 p.m.