Skip to contents

Run stabilised (multi-run) NMF on the GPU over single cell or meta cell data

stabilised_nmf_gpu_sc.Rd

GPU counterpart of bixverse::stabilised_nmf_sc(). Runs n_runs HALS NMF with random initialisations seeded by seed + i. The nmf_init field in nmf_hals_params is ignored; random init is always used.

The counts upload once and serve every restart, but the restarts themselves run one after the other on the single device, where the CPU version spreads them across cores. On a small matrix the CPU can still win.

Usage

stabilised_nmf_gpu_sc(
  object,
  k,
  cell_ids = NULL,
  gene_ids = NULL,
  preprocessing = "none",
  use_second_layer = TRUE,
  nmf_hals_params = bixverse::params_nmf_hals(),
  n_runs = 30L,
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells or MetaCells class from bixverse.

k

Integer. Number of latent factors per run. At most 128, see NMF_GPU_MAX_RANK.

cell_ids

Optional character. Cell ids (or meta cell ids) to restrict the NMF to. If NULL, uses bixverse::get_cells_to_keep() for SingleCells and all meta cells for MetaCells.

gene_ids

Optional character. Gene ids to restrict the NMF to. If NULL, uses bixverse::get_hvg() on the object.

preprocessing

String. One of c("none", "sd", "sqrt_sd").

use_second_layer

Boolean. If TRUE, runs NMF on the normalised counts (recommended); if FALSE, on the raw counts.

nmf_hals_params

List, see bixverse::params_nmf_hals().

n_runs

Integer. Number of random restarts.

seed

Integer. Random seed for initialisation.

.verbose

Boolean or integer. Controls verbosity. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

A StabilisedNmfResult object, the same class bixverse::stabilised_nmf_sc() returns.