Cell-feature coembedding for scRNA-seq data

Cell-feature coembedding for scRNA-seq data based on FAST model.

NCFM(
  object,
  assay = NULL,
  slot = "data",
  nfeatures = 2000,
  q = 10,
  reduction.name = "ncfm",
  weighted = FALSE,
  var.features = NULL
)

Arguments

object: a Seurat object.
assay: an optional string, specify the name of assay in the Seurat object to be used, `NULL` means default assay in seu.
slot: an optional string, specify the name of slot.
nfeatures: an optional integer, specify the number of features to select as top variable features. Default is 2000.
q: an optional positive integer, specify the dimension of low dimensional embeddings to compute and store. Default is 10.
reduction.name: an optional string, specify the dimensional reduction name, `ncfm` by default.
weighted: an optional logical value, specify whether use weighted method.
var.features: an optional string vector, specify the variable features used to calculate cell embedding.

data(pbmc3k_subset)
pbmc3k_subset <- NCFM(pbmc3k_subset)
#> 2024-03-17 18:26:34 : ***** Finish CoFAST, 0.008 mins elapsed.