computeDC: Dimensionality reduction using diffusion components.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Dimensionality reduction using diffusion components.

Description

Performs dimensionality reduction using the DiffusionMap function from the destiny package. The destiny package is presenting errors in the installation, so it is not imported in the description.

Usage

computeDC(
  object,
  assay.type = "RNA",
  genes.use = NULL,
  k = 20,
  sigma = "local",
  seed = 1
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
genes.use	character vector; genes used in diffusion components dimensionality reduction. The default is all genes in normalized data.
k	numeric; parameter k to be used by the DiffusionMap function from destiny pakcage.
sigma	character; parameter sigma to be used by the DiffusionMap function from destiny pakcage.
seed	numeric; random seed.

Value

CellRouter object with the dc slot updated.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.