makeExampleData {EnrichmentBrowser} | R Documentation

## Example data for the EnrichmentBrowser package

### Description

Functionality to construct example data sets for demonstration. This includes expression data, gene sets, gene regulatory networks, and enrichment analysis results.

### Usage

    makeExampleData(what = c("SE", "gs", "grn", "ea.res"), ...)

### Arguments

`what` | Kind of example data set to be constructed. This should be one out of: SE: SummarizedExperiment gs: Gene set list grn: Gene regulatory network ea.res: Enrichment analysis result object as returned by the functions `sbea` and `nbea`
`...` | Additional arguments to fine-tune the specific example data sets. For what='SE': type: Expression data type. Should be either 'ma' (Microarray intensity measurements) or 'rseq' (RNA-seq read counts). nfeat: Number of features/genes. Defaults to 100. nsmpl: Number of samples. Defaults to 12. blk: Create sample blocks. Defaults to TRUE. norm: Should the expression data be normalized? Defaults to FALSE. deAna: Should an differential expression analysis be carried out automatically? Defaults to FALSE. For what='gs': gnames: gene names from which the sets will be sampled. Per default the sets will be drawn from c(g1, ..., g100). n: number of sets. Defaults to 10. min.size: minimal set size. Defaults to 15. max.size: maximal set size. Defaults to 25. For what='grn': nodes: gene node names for which edges will be drawn. Per default node names will be c(g1, ..., g100). edge.node.ratio: ratio number of edges / number of nodes. Defaults to 3, i.e. creates 3 times more edges than nodes. For what='ea.res': SE: SummarizedExperiment. Calls makeExampleData(what="SE") per default. gs: Gene sets. Calls makeExampleData(what="gs") per default. method: Enrichment analysis method. Defaults to 'ora'. alpha: Statistical significance level. Defaults to 0.05.

### Value

Depends on the 'what' argument.

### Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

### Examples

        se <- makeExampleData(what="SE")

[Package EnrichmentBrowser version 2.16.1 Index]