Read_Add_cNMF: Read and add results from cNMF

In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Read and add results from cNMF

Description

Reads the usage and spectra files from cNMF results and adds them as dimensionality reduction to seurat object.

Usage

Read_Add_cNMF(
  seurat_object,
  usage_file,
  spectra_file,
  reduction_name = "cnmf",
  reduction_key = "cNMF_",
  normalize = TRUE,
  assay = NULL,
  overwrite = FALSE
)

Arguments

seurat_object	Seurat object name to add cNMF reduction
usage_file	path and name of cNMF usage file
spectra_file	path and name of cNMF spectra file
reduction_name	name to use for reduction to be added, default is "cnmf".
reduction_key	key to use for reduction to be added, default is "cNMF_".
normalize	logical, whether to normalize the cNMF usage data, default is TRUE
assay	assay to add reduction. Default is NULL and will use current active assay.
overwrite	logical, whether to overwrite a reduction with the name reduction_name already present in reduction slot of given Seurat object.

Value

Seurat object with new dimensionality reduction "cnmf"

References

For more information about cNMF and usage see https://github.com/dylkot/cNMF

Examples

## Not run: 
object <- Read_cNMF(seurat_object = object,
usage_file = "example_cNMF/example_cNMF.usages.k_27.dt_0_01.consensus.txt",
spectra_file = "example_cNMF/example_cNMF.gene_spectra_score.k_27.dt_0_01.txt")

## End(Not run)

scCustomize documentation built on Dec. 11, 2025, 5:08 p.m.