annotatePeak: annotatePeak

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

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,
  columns = c("ENTREZID", "ENSEMBL", "SYMBOL", "GENENAME")
)

Arguments

peak	peak file or GRanges object
tssRegion	Region Range of TSS
TxDb	TxDb or EnsDb annotation 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
columns	names of columns to be obtained from database

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)

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.