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

In shmohammadi86/ACTIONetExperiment: ACTIONetExperiment container object

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.