assignGeneID {CAGEfightR} | R Documentation

## Annotate ranges with gene ID.

### Description

Annotate a set of ranges in a GRanges object with gene IDs (i.e. Entrez Gene Identifiers) based on their genic context. Features overlapping multiple genes are resolved by distance to the nearest TSS. Genes are obtained from a TxDb object, or can manually supplied as a GRanges.

### Usage

    assignGeneID(object, geneModels, ...)

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    assignGeneID(
      object,
      geneModels,
      outputColumn = "geneID",
      swap = NULL,
      upstream = 1000,
      downstream = 100
    )

    ## S4 method for signature 'RangedSummarizedExperiment,GenomicRanges'
    assignGeneID(object, geneModels, ...)

    ## S4 method for signature 'GenomicRanges,TxDb'
    assignGeneID(
      object,
      geneModels,
      outputColumn = "geneID",
      swap = NULL,
      upstream = 1000,
      downstream = 100
    )

    ## S4 method for signature 'RangedSummarizedExperiment,TxDb'
    assignGeneID(object, geneModels, ...)

### Arguments

`object` | GRanges or RangedSummarizedExperiment: Ranges to be annotated.
`geneModels` | TxDb or GRanges: Gene models via a TxDb, or manually specified as a GRangesList.
`...` | additional arguments passed to methods.
`outputColumn` | character: Name of column to hold geneID values.
`swap` | character or NULL: If not NULL, use another set of ranges contained in object to calculate overlaps, for example peaks in the thick column.
`upstream` | integer: Distance to extend annotated promoter upstream.
`downstream` | integer: Distance to extend annotated promoter downstream.

### Value

object with geneID added as a column in rowData (or mcols).

### See Also

Other Annotation functions: `assignMissingID()`, `assignTxID()`, `assignTxType()`

### Examples

    data(exampleUnidirectional)

    # Obtain gene models from a TxDb-object:
    library(TxDb.Mmusculus.UCSC.mm9.knownGene)
    txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene

    # Assign geneIDs
    assignGeneID(exampleUnidirectional,
                 geneModels=txdb,
                 outputColumn='geneID')

    # Assign geneIDs using only TC peaks:
    assignGeneID(exampleUnidirectional,
                 geneModels=txdb,
                 outputColumn='geneID',
                 swap='thick')

[Package CAGEfightR version 1.10.0 Index]