makeExampleData: Example data for the EnrichmentBrowser package

In lgeistlinger/EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

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

Examples

    se <- makeExampleData(what="SE")

lgeistlinger/EnrichmentBrowser documentation built on Oct. 29, 2023, 5:08 p.m.