seurat_to_scMinimal: Convert Seurat object to scMinimal object. Generally, this...

In scITD: Single-Cell Interpretable Tensor Decomposition

Convert Seurat object to scMinimal object. Generally, this should be done through calling the make_new_container() wrapper function.

Description

Convert Seurat object to scMinimal object. Generally, this should be done through calling the make_new_container() wrapper function.

Usage

seurat_to_scMinimal(seurat_obj, metadata_cols = NULL, metadata_col_nm = NULL)

Arguments

seurat_obj	Seurat object that has been cleaned and includes the normalized, log-transformed counts. The meta.data should include a column with the header 'sex' and values of 'M' or 'F' if available. The metadata should also have a column with the header 'ctypes' with the corresponding names of the cell types as well as a column with header 'donors' that contains identifiers for each donor.
metadata_cols	character The names of the metadata columns to use (default=NULL)
metadata_col_nm	character New names for the selected metadata columns if wish to change their names. If NULL, then the preexisting column names are used. (default=NULL)

Value

An scMinimal object holding counts and metadata for a project.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.