Description
Usage
Arguments
Value
Author(s)
Examples
View source: R/examples.R
Functionality to construct example data sets for demonstration. This
includes expression data, gene sets, gene regulatory networks, and
enrichment analysis results.
| (what = ("SE", "gs", "grn", "ea.res"), )
|
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':
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.
|
Depends on the 'what' argument.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
EnrichmentBrowser documentation built on Dec. 12, 2020, 2 a.m.
