mcell_import_multi_scmat_10x: Load a matrix from a 10x multi-batch dataset. The scdb...

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

Load a matrix from a 10x multi-batch dataset. The scdb version of mcell_read_multi_scmat_10x

Description

Load a matrix from a 10x multi-batch dataset. The scdb version of mcell_read_multi_scmat_10x

Usage

mcell_import_multi_scmat_10x(mat_nm, dataset_table_fn, base_dir, force = FALSE)

Arguments

mat_nm	- the name of the new matrix in scdb
dataset_table_fn	- The index file of the 10x multi batch dataset. Fileds include: Batch.Set.ID, mat_fn, genes_fn, cells_fn. The first field must be specifieid for each row. The others may be NA, in which case the import process will search for base_dir/Batch.Set.ID/matrix.mtx, genes.tsv (or features.tsv), barcodes.tsv.
base_dir	- directory where raw 10x files are located (dataset table points to subdirectories of this)
force	- if true, will import from 10x files even when the matrix is present in the DB

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.