Get factor matrices from a BulkModuleResult — get

Returns one factor matrix by key, or the whole named list of factor matrices if which is NULL. Keys are method-specific; see the factors argument of new_bulk_module_result() for the shared vocabulary.

Usage

get_factors(object, which = NULL)

Arguments

object: A BulkModuleResult.
which: String or NULL. Name of the factor matrix to return. If NULL, returns the whole list.

Value

A matrix, the named list of matrices, or NULL (with warning) if which is not among the stored factor keys.

Examples

# gene loadings and sample activities of an NMF fit
syn <- synthetic_bulk_cor_matrix()
mat <- log1p(t(syn$counts))
meta <- data.table::data.table(sample_id = rownames(mat))
object <- BulkCoExp(raw_data = mat, meta_data = meta)
object <- preprocess_bulk_coexp(object, hvg = 500L, .verbose = FALSE)
object <- nmf_bulk(object, k = 3L, .verbose = FALSE)
res <- S7::prop(object, "final_results")
names(get_factors(res))
#> [1] "gene_loadings"   "sample_activity"
dim(get_factors(res, "gene_loadings"))
#> [1] 500   3