scrat.run: Execute the scrat pipeline.

In hloefflerwirth/scrat: Single Cell - R Analysis Toolbox

Execute the scrat pipeline.

Description

This function realizes the complete pipeline functionality: single gene expression values are culstered to metagenes using a self-organizing map. Based on these metagenes, visualizations (e.g. expression portraits), downstreaming sample similarity analyses (e.g. hierarchical clustering, ICA) and pseudotime analysis are performed. The results are given within a separate folder and can be browsed using the summary HTML file.

Usage

scrat.run(env)

Arguments

env	the scrat environment created with scrat.new according to the users' preferences

Examples

# Example with artificial data
env <- scrat.new(list(dataset.name="Example",
                        dim.1stLvlSom=10))

env$indata <- matrix(runif(1000), 100, 10)

scrat.run(env)

hloefflerwirth/scrat documentation built on Sept. 2, 2022, 4:09 a.m.