geneSets {sparrow} | R Documentation

## Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult

### Description

Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult

### Usage

    geneSets(x, ...)

    ## S4 method for signature 'GeneSetDb'
    length(x)

    ## S4 method for signature 'GeneSetDb'
    geneSets(x, active.only = is.conformed(x), ..., as.dt = FALSE)

    ## S4 method for signature 'GeneSetDb'
    nrow(x)

    ## S4 method for signature 'SparrowResult'
    geneSets(x, ..., as.dt = FALSE)

### Arguments

`x` | Object to retrieve the gene set from, either a `GeneSetDb` or a `SparrowResult`.
`...` | pass through arguments
`active.only` | only look for gene sets that are "active"? Defaults to `TRUE` if `x` is conformed to a target expression object, else `FALSE`. `conform()` for further details.
`as.dt` | If `FALSE` (default), the data.frame like thing that this funciton returns will be set to a data.frame. Set this to `TRUE` to keep this object as a `data.table`

### Value

a data.table with geneset information.

### Methods (by class)

- `GeneSetDb`: Returns the number of genesets in a GeneSetDb

- `GeneSetDb`: return all genesets from a GeneSetDb

- `GeneSetDb`: return number of genesets in GeneSetDb

- `SparrowResult`: return the active genesets from a SparrowResult

### Examples

    gdb <- exampleGeneSetDb()
    gs <- geneSets(gdb)

[Package sparrow version 1.0.3 Index]