ProFAST (version 1.4)

NCFM: Cell-feature coembedding for scRNA-seq data

Description

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

Usage

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.

Examples

data(pbmc3k_subset)
pbmc3k_subset <- NCFM(pbmc3k_subset)