assignTxID {CAGEfightR} | R Documentation

## Annotate ranges with transcript ID.

### Description

Annotate a set of ranges in a GRanges object with transcript IDs based on their genic context. All overlapping transcripts are returned. Transcripts are obtained from a TxDb object, or can manually supplied as a GRanges.

### Usage

    assignTxID(object, txModels, ...)

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    assignTxID(object, txModels, outputColumn = "txID", swap = NULL)

    ## S4 method for signature 'RangedSummarizedExperiment,GenomicRanges'
    assignTxID(object, txModels, ...)

    ## S4 method for signature 'GenomicRanges,TxDb'
    assignTxID(
      object,
      txModels,
      outputColumn = "txID",
      swap = NULL,
      upstream = 1000,
      downstream = 0
    )

    ## S4 method for signature 'RangedSummarizedExperiment,TxDb'
    assignTxID(object, txModels, ...)

### Arguments

`object` | GRanges or RangedSummarizedExperiment: Ranges to be annotated.
`txModels` | TxDb or GRanges: Transcript models via a TxDb, or manually specified as a GRanges.
`...` | additional arguments passed to methods.
`outputColumn` | character: Name of column to hold txID 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 txID added as a column in rowData (or mcols)

### See Also

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

### Examples

    data(exampleUnidirectional)

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

    # Assign txIDs
    assignTxID(exampleUnidirectional,
               txModels=txdb,
               outputColumn='geneID')

    # Assign txIDs using only TC peaks:
    assignTxID(exampleUnidirectional,
                 txModels=txdb,
                 outputColumn='geneID',
                 swap='thick')

[Package CAGEfightR version 1.10.0 Index]