ACTIONetExperiment: ACTIONet: Robust multi-resolution analysis of single-cell...

View source: R/AllClasses.R

ACTIONetExperimentR Documentation

ACTIONet: Robust multi-resolution analysis of single-cell datasets

Description

Joint archetypal/network-based analysis for multi-resolution decomposition of single-cell states.

Usage

ACTIONetExperiment(
  ...,
  rowNets = S4Vectors::SimpleList(),
  colNets = S4Vectors::SimpleList(),
  rowMaps = S4Vectors::SimpleList(),
  colMaps = S4Vectors::SimpleList()
)

Arguments

...

SummarizedExperiment and SummarizedExperiment components

rowNets, colNets

gene-gene and cell-cell networks, respectively

rowMaps, colMaps

Factorization results (W and H matrices)

Value

an ACTIONetExperiment (ACE) object

An ACTIONetExperiment (ACE) object, derived from SummarizedExperiment, with additional slots to store ACTIONet results

Slots

rowNets,colNets

gene-gene and cell-cell networks, respectively

rowMaps,colMaps

Factorization results (W and H matrices)

Usage

  1. ?reduce.sce to reduce raw count matrix in an SummarizedExperiment objects.

  2. ?run.ACTIONet to run ACTIONet on SummarizedExperiment objects.

Useful links

  1. Report bugs at https://github.com/shmohammadi86/ACTIONet/issues

  2. Read the manuscript: A multiresolution framework to characterize single-cell state landscapes.

Author(s)

Shahin Mohammadi


shmohammadi86/ACTIONetExperiment documentation built on Sept. 13, 2023, 8:55 p.m.