opossom.run {oposSOM} | R Documentation

## 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 portraits), 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)

[Package oposSOM version 2.4.0 Index]