makeExampleData: Example data for the EnrichmentBrowser package
In EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Functionality to construct example data sets for demonstration. This
includes expression data, gene sets, gene regulatory networks, and
enrichment analysis results.
Usage
1
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
1
se <- makeExampleData(what="SE")
EnrichmentBrowser documentation built on Dec. 12, 2020, 2 a.m.
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Description Usage Arguments Value Author(s) Examples
Description
Functionality to construct example data sets for demonstration. This includes expression data, gene sets, gene regulatory networks, and enrichment analysis results.
Usage
1 | makeExampleData(what = c("SE", "gs", "grn", "ea.res"), ...)
|
Arguments
what |
Kind of example data set to be constructed. This should be one out of:
|
... |
Additional arguments to fine-tune the specific example data sets. For what='SE':
For what='gs':
For what='grn':
For what='ea.res':
|
Value
Depends on the 'what' argument.
Author(s)
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
Examples
1 | se <- makeExampleData(what="SE")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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