R: Annotate ranges with transcript ID.

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)

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')