scToNeb: Retrieve data from Seurat or SingleCellExperiment object to...

In nebula: Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

Retrieve data from Seurat or SingleCellExperiment object to prepare for use in nebula

Description

Extracts count matrix and metadata from Seurat or SingleCellExperiment objects and formats them for use with the nebula function. Handles predictors, sample IDs, and offset factors.

Usage

scToNeb(
  obj,
  assay = NULL,
  id = NULL,
  pred = NULL,
  offset = NULL,
  verbose = TRUE
)

Arguments

obj	Seurat or SingleCellExperiment object to create data set for Nebula.
assay	Assay to retrieve counts from the corresponding Seurat count matrix.
id	Sample ID to use metadata object i.e. obj$id.
pred	Character vector of predictors from metadata in Seurat or SingleCellExperiment objects.
offset	Metadata column corresponding to per-cell scaling factor e.g. TMM.
verbose	Indicating whether to print additional messages.

Details

Retrieve data from Seurat or SingleCellExperiment object to prepare for use in nebula

Value

data_neb: A list usable for nebula.

Examples

## Not run: 
library(Seurat)
library(nebula)

sample_seurat <- load_sample_seurat()
re <- scToNeb(obj = sample_seurat, assay = "RNA", id = "replicate", pred = c("celltype", "tech"))

## End(Not run)

nebula documentation built on July 12, 2026, 9:06 a.m.