assignGeneID: Annotate ranges with gene ID.

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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')

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.