runNMF {GeneNMF}

Compute NMF as a low-dim embedding for Seurat

Description

Compute NMF embeddings for single-cell dataset, and store them in the Seurat data structure. They can be used as an alternative to PCA for downstream analyses.

Usage

runNMF(
  obj,
  assay = "RNA",
  slot = "data",
  k = 10,
  new.reduction = "NMF",
  seed = 123,
  L1 = c(0, 0),
  hvg = NULL,
  center = FALSE,
  scale = FALSE
)

Arguments

obj

A seurat object

assay

Get data matrix from this assay

slot

Get data matrix from this slot (=layer)

k

Number of components for low-dim representation

new.reduction

Name of new dimensionality reduction

seed

Random seed

L1

L1 regularization term for NMF

hvg

Which genes to use for the reduction

center

Whether to center the data matrix

scale

Whether to scale the data matrix

Value

Returns a Seurat object with a new dimensionality reduction (NMF)

Examples

data(sampleObj)
sampleObj <- runNMF(sampleObj, k=8)