annotatePeak {ChIPseeker} | R Documentation

## annotatePeak

### Description

Annotate peaks

### Usage

    annotatePeak(peak, tssRegion = c(-3000, 3000), TxDb = NULL,
      level = "transcript", assignGenomicAnnotation = TRUE,
      genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron",
      "Downstream", "Intergenic"), annoDb = NULL, addFlankGeneInfo = FALSE,
      flankDistance = 5000, sameStrand = FALSE, ignoreOverlap = FALSE,
      ignoreUpstream = FALSE, ignoreDownstream = FALSE, overlap = "TSS",
      verbose = TRUE)

### Arguments

`peak` | peak file or GRanges object
`tssRegion` | Region Range of TSS
`TxDb` | TxDb object
`level` | one of transcript and gene
`assignGenomicAnnotation` | logical, assign peak genomic annotation or not
`genomicAnnotationPriority` | genomic annotation priority
`annoDb` | annotation package
`addFlankGeneInfo` | logical, add flanking gene information from the peaks
`flankDistance` | distance of flanking sequence
`sameStrand` | logical, whether find nearest/overlap gene in the same strand
`ignoreOverlap` | logical, whether ignore overlap of TSS with peak
`ignoreUpstream` | logical, if True only annotate gene at the 3' of the peak.
`ignoreDownstream` | logical, if True only annotate gene at the 5' of the peak.
`overlap` | one of 'TSS' or 'all', if overlap="all", then gene overlap with peak will be reported as nearest gene, no matter the overlap is at TSS region or not.
`verbose` | print message or not

### Value

data.frame or GRanges object with columns of:

all columns provided by input.

annotation: genomic feature of the peak, for instance if the peak is located in 5'UTR, it will annotated by 5'UTR. Possible annotation is Promoter-TSS, Exon, 5' UTR, 3' UTR, Intron, and Intergenic.

geneChr: Chromosome of the nearest gene

geneStart: gene start

geneEnd: gene end

geneLength: gene length

geneStrand: gene strand

geneId: entrezgene ID

distanceToTSS: distance from peak to gene TSS

if annoDb is provided, extra column will be included:

ENSEMBL: ensembl ID of the nearest gene

SYMBOL: gene symbol

GENENAME: full gene name

### Author(s)

G Yu

### See Also

`plotAnnoBar` `plotAnnoPie` `plotDistToTSS`

### Examples

    ## Not run:
    require(TxDb.Hsapiens.UCSC.hg19.knownGene)
    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
    peakfile <- system.file("extdata", "sample_peaks.txt", package="ChIPseeker")
    peakAnno <- annotatePeak(peakfile, tssRegion=c(-3000, 3000), TxDb=txdb)
    peakAnno

    ## End(Not run)

[Package ChIPseeker version 1.14.2 Index]