annotatePeak
Annotate peaks
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
)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 |
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
G Yu
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.