ChIPseeker (version 1.2.6)

annotatePeak: annotatePeak

Description

Annotate peaks

Usage

annotatePeak(peak, tssRegion = c(-3000, 3000), TxDb = NULL, level = "transcript", assignGenomicAnnotation = TRUE, annoDb = NULL, addFlankGeneInfo = FALSE, flankDistance = 5000, 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

annoDb

annotation package

addFlankGeneInfo

logical, add flanking gene information from the peaks

flankDistance

distance of flanking sequence

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 genegeneStart: gene startgeneEnd: gene endgeneLength: gene lengthgeneStrand: gene strandgeneId: entrezgene IDdistanceToTSS: distance from peak to gene TSSif annoDb is provided, extra column will be included:ENSEMBL: ensembl ID of the nearest geneSYMBOL: gene symbolGENENAME: full gene name

See Also

plotAnnoBar plotAnnoPie plotDistToTSS

Examples

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