exampleExpressionSet {sparrow} | R Documentation

## 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())

[Package sparrow version 1.0.3 Index]