Get the NMF gene loadings — get_nmf_gene

Getter function to extract the gene loadings matrix (features x k) from a bulk NMF fit stored in BulkCoExp(). If no NMF fit is present, returns NULL with a warning.

Usage

get_nmf_gene_loadings(object)

Arguments

object: The class, see BulkCoExp().

Value

A features x k numeric matrix (if found) or NULL.

Examples

# gene loadings of a four-factor fit
syn <- generate_gene_module_data(n_samples = 24L, n_genes = 60L)
# NMF needs a non-negative matrix
mat <- syn$data - min(syn$data)
obj <- BulkCoExp(mat, syn$meta_data)
obj <- preprocess_bulk_coexp(
  obj, hvg = NULL, scaling = FALSE, .verbose = FALSE
)
obj <- nmf_bulk(obj, k = 4L, .verbose = FALSE)
dim(get_nmf_gene_loadings(obj))
#> [1] 60  4