dot-GenerateSizeFactor: .GenerateSizeFactor

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

.GenerateSizeFactor

Description

A helper function for ConstructEnrichmentDataFrameAndDoStatistics that calculates size factors for differently sized scRNA-Seq datasets.

Usage

.GenerateSizeFactor(
  seuratObj,
  normalizationField = "cDNA_ID",
  sizeFactorField = "SizeFactor",
  maxSizeFactor = 100
)

Arguments

seuratObj	The seurat object that holds the data.
normalizationField	The metadata column that is used for size factor calculation (equivalently, normalization between different datasets.) Recommended to be cDNA_ID.
sizeFactorField	The column name of the seruat object metadata that size factors should be stored in.
maxSizeFactor	The maximum allowable SizeFactor before an error is automatically thrown. For instance, a size factor of 100 means you have a group of 8000 cells that you're comparing to 80 cells.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.