Example data for the EnrichmentBrowser package

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Description

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

Usage

1
    make.example.data( what = c("eset", "gs", "grn", "ea.res"), ... )

Arguments

what

Kind of example data set to be constructed. This should be one out of:

  • eset: Expression set

  • 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='eset':

  • 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.

  • de.ana: 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':

  • eset: Expression set. Calls make.example.data(what="eset") per default.

  • gs: Gene sets. Calls make.example.data(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@bio.ifi.lmu.de>

Examples

1
    eset <- make.example.data(what="eset")