RPeakAnno: Annotate ATAC-seq Peak

RPeakAnnoR Documentation

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/esATAC documentation built on Aug. 12, 2022, 7:41 a.m.