NCFM: Cell-feature coembedding for scRNA-seq data

In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

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)

ProFAST documentation built on April 3, 2025, 7:51 p.m.