Generate multi-level hierarchical single-cell reference (`hscreference`) object
new_hscreference.RdGenerate multi-level hierarchical single-cell reference (`hscreference`) object
Usage
new_hscreference(
seurat_obj,
annot_ids,
batch_id = NULL,
project_name = "project",
cache_path = "scref_cache",
sample_cells = NULL,
seed = NULL
)Arguments
- seurat_obj
a reference Seurat object
- annot_ids
in order, column names of the Seurat object metadata from coarsest to finest grained annotation
- batch_id
NULL or a column name of the Seurat object metadata containing information about batch to be used as batch information downstream. Examples of batch are patient ID, study ID, etc.
- project_name
a string indicating the project name, used for caching
- cache_path
path to the directory where results will be cached
- sample_cells
NULL or a list with how many cells to randomly sub-sample of each population in the coarsest grained annotation. Sub-sampling can make the object significantly smaller and accelerate downstream computation, but make the results less accurate.
- seed
an integer representing a "seed", for reproducibility of sub-sampling.