geneSet {sparrow} | R Documentation

## Fetches information for a gene set

### Description

Gene sets inside a `GeneSetDb()` are indexed by their collection,name compound key. There is no special class to represent an individual gene set. Instead, gene sets are returned as a data.frame, the rows of which enumerate the features that belong to them.

When `x` is a `SparrowResult()`, this function will append the differential expression statistics for the individual features generated across the contrast that defined `x`.

### Usage

    geneSet(x, i, j, ...)

    ## S4 method for signature 'GeneSetDb'
    geneSet(
      x,
      i,
      j,
      active.only = is.conformed(x),
      with.feature.map = FALSE,
      ...,
      collection = NULL,
      name = NULL,
      as.dt = FALSE
    )

    ## S4 method for signature 'SparrowResult'
    geneSet(
      x,
      i,
      j,
      active.only = TRUE,
      with.feature.map = FALSE,
      ...,
      collection = NULL,
      name = NULL,
      as.dt = FALSE
    )

### Arguments

`x` | Object to retrieve the gene set from, either a `GeneSetDb` or a `SparrowResult`.
`i` | The collection,name compound key identifier of the gene set
`j` | The collection,name compound key identifier of the gene set
`...` | passed down to inner functinos
`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.
`with.feature.map` | If `TRUE`, then details of the feature mapping from the original feature_id space to the target feature space are included (default: `FALSE`).
`collection` | using `i` as the parameter for "collection" isn't intuitive so if speficially set this paramter, it will replace the value for `i`.
`name` | the same for the `collection`:`i` parameter relationship, but for `j`:`name`.
`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.(frame|table)` of gene set information. If `x` is a `SparrowResult` object, then differential expression statistics are added as columns to this result.

### Examples

    gdb <- exampleGeneSetDb()
    geneSet(gdb, "c2", "KOMMAGANI_TP63_GAMMA_TARGETS")
    geneSet(gdb, collection = "c2", name = "KOMMAGANI_TP63_GAMMA_TARGETS")
    geneSet(gdb, name = "KOMMAGANI_TP63_GAMMA_TARGETS")

[Package sparrow version 1.0.3 Index]