nebula (version 1.5.6)

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

Description

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

Usage

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

Value

data_neb: A list usable for nebula.

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.

Examples

if (FALSE) {
library(Seurat)
library(nebula)

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