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,
  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

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")
}