RPeakAnno: Annotate ATAC-seq Peak

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Annotate ATAC-seq Peak

Description

This function annotates ATAC-seq peak by a given annotation database. For more information, please see annotatePeak.

Usage

atacPeakAnno(
  atacProc,
  peakInput = NULL,
  tssRegion = c(-1000, 1000),
  TxDb = NULL,
  level = "transcript",
  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",
  annoOutput = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacPeakAnno(
  atacProc,
  peakInput = NULL,
  tssRegion = c(-1000, 1000),
  TxDb = NULL,
  level = "transcript",
  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",
  annoOutput = NULL,
  ...
)

peakanno(
  peakInput,
  tssRegion = c(-1000, 1000),
  TxDb = NULL,
  level = "transcript",
  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",
  annoOutput = NULL,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacPeakCalling.
peakInput	Character scalar. Input peak file path. UCSC bed file is recommented. Other file should be able to import as GRanges objects through import in package rtracklayer.
tssRegion	Region range of TSS, default:c(-1000, 1000).
TxDb	TxDb object, annotation database.
level	"transcript" or "gene".
genomicAnnotationPriority	genomic annotation priority.
annoDb	Gene annotation database.
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.
annoOutput	Character scalar. the output file path.
...	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

References

Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383

See Also

atacPeakCalling atacGOAnalysis

Examples

library(R.utils)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
peak1_path <- as.vector(bunzip2(filename = p1bz,
destname = file.path(getwd(), "Example_peak1.bed"),
ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
#peakanno(peakInput = peak1_path, TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene,
#annoDb = 'org.Hs.eg.db')

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.