Functions that load data for use in examples and testing.

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

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

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

exampleGeneSetDb()

exampleGeneSetDF()

exampleMultiGSEAResult(cached = TRUE)

exampleDgeResult(species = "human", id.type = "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.

Value

A list of lists of entrezIDs when as == 'lol', or a list of integers into the rows of exampleExpressionSet for the genes in the given geneset.

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 or integers that index into a target expression object x.

exampleGeneSetDb

Returns gene sets as a GeneSetDb object

exampleGeneSetDF

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