assignTxID: Annotate ranges with transcript ID.

Description Usage Arguments Value See Also Examples

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

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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

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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')

MalteThodberg/CAGEfightR documentation built on May 8, 2019, 3:36 p.m.