Read and add results from cNMF — Read_Add

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

Read_Add_cNMF(
  seurat_object,
  usage_file,
  spectra_file,
  normalize = TRUE,
  assay = NULL
)

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
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.

Value

Seurat object with new dimensionality reduction "cnmf"

References

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

Examples

if (FALSE) {
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")
}