examples: Functions that load data for use in examples and testing.

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

Functions that load data for use in examples and testing.

Description

We provide examplar expression data (counts or voomed) as well as exemplar gene sets in different forms.

Usage

exampleExpressionSet(
  dataset = c("tumor-vs-normal", "tumor-subtype"),
  do.voom = TRUE
)

exampleGeneSets(x, unlist = !missing(x))

exampleGeneSetDb()

exampleBiocSet()

exampleGeneSetDF()

exampleSparrowResult(cached = TRUE, methods = c("cameraPR", "fry"))

exampleDgeResult(
  species = "human",
  id.type = c("entrez", "ensembl"),
  induce.bias = NULL
)

Arguments

dataset	Character vector indicating what samples wanted, either "tumor-vs-normal" for a tumor vs normal dataset from TCGA, or just the tumor samples from the same annotated with subtype.
do.voom	If TRUE, a voomed EList is returned, otherwise an ExpressionSet of counts.
x	If provided, an expression/matrix object so that the genesets are returned as (integer) index vectors into the rows of x whose rownames match the ids in the geneset.
unlist	return the genesets as nested list of lists (default: TRUE). The top level lists corresponds to the collection, and the lists within each are the inidividual gene sets. If FALSE, a single list of genesets is returned.
cached	If TRUE (default), returns a pre-saved SparrowResult object. Otherwise calculates a fresh one using the methods provided
methods	the methods to use to create a new SparrowResult for.
species	the species to return the example result from (right now, only "human")
id.type	the type of identifiers to use: "entrez" (default) or "ensembl".
induce.bias	We can simulate a bias on the pvalue by the gene's "effective_length" or "AveExpr". These are columns that are included in the output. If NULL, no bias is introduced into the result.

Value

A list of lists of entrezIDs when as == 'lol', or a list of integers into the rows of x.

exampleExpressionSet

The expression data is a subset of the TCGA BRCA indication. Calling exampleExpressionSet(do.voom = TRUE) will return a voomed EList version of the data. When do.voom = FALSE, you will get a DGEList of the counts

exampleGeneSets

Returns gene sets as either a list of feature identifiers. Entrez identifiers are used. If x is provided, integers that index into the expression container x are used (this is a legacy feature that we should nuke).

exampleGeneSetDb

Returns gene sets as a GeneSetDb object

exampleBiocSet

Returns gene sets as a BiocSet object

exampleGeneSetDF

Returns a data.frame of gene set definitions. A data.frame of this form can be passed into the GeneSetDb() contructor.

Examples

vm <- exampleExpressionSet()
head(exampleGeneSets())

lianos/sparrow documentation built on Aug. 8, 2024, 9:01 a.m.