Get the NMF sample activity

Getter function to extract the sample activity matrix (samples x k) from a bulk NMF fit. If no NMF fit is present, returns NULL with a warning.

Usage

get_nmf_sample_activity(object)

Arguments

object

The class, see BulkCoExp().

Value

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

Examples

# sample activity 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_sample_activity(obj))
#> [1] 24  4