oposSOM (version 1.10.0)

opossom.run: Execute the oposSOM 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 profiles), downstreaming sample similarity analyses (e.g. hierarchical clustering, ICA) and functional enrichment analyses are performed. The results are given within a separate folder and can be browsed using the summary HTML file.

Usage

opossom.run(env)

Arguments

env

the opossom environment created with opossom.new according to the users' preferences

Examples

# Example with artificial data
env <- opossom.new(list(dataset.name="Example",
                        dim.1stLvlSom=20))

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

opossom.run(env)