findEnhancers: Find possible enhancers depend on DNA interaction data

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Find possible enhancers depend on DNA interaction data

Description

Find possible enhancers by data from chromosome conformation capture techniques such as 3C, 5C or HiC.

Usage

findEnhancers(
  peaks,
  annoData,
  DNAinteractiveData,
  bindingType = c("nearestBiDirectionalPromoters", "startSite", "endSite"),
  bindingRegion = c(-5000, 5000),
  ignore.peak.strand = TRUE,
  ...
)

Arguments

peaks	peak list, GRanges object
annoData	annotation data, GRanges object
DNAinteractiveData	DNA interaction data, GRanges object with interaction blocks informations, GInteractions object, or BEDPE file which could be imported by importGInteractions or BiocIO::import or assembly in following list: hg38, hg19, mm10, danRer10, danRer11.
bindingType	Specifying the criteria to associate peaks with annotation. Here is how to use it together with the parameter bindingRegion. The annotation will be shift to a new position depend on the DNA interaction region. To obtain peaks within 5kb upstream and up to 3kb downstream of shift TSS within the gene body, set bindingType = "startSite" and bindingRegion = c(-5000, 3000) To obtain peaks up to 5kb upstream within the gene body and 3kb downstream of shift gene/Exon End, set bindingType = "endSite" and bindingRegion = c(-5000, 3000) To obtain peaks with nearest bi-directional enhancer regions within 5kb upstream and 3kb downstream of shift TSS, set bindingType = "nearestBiDirectionalPromoters" and bindingRegion = c(-5000, 3000) startSite start position of the feature (strand is considered) endSite end position of the feature (strand is considered) nearestBiDirectionalPromoters nearest enhancer regions from both direction of the peaks (strand is considered). It will report bidirectional enhancer regions if there are enhancer regions in both directions in the given region (defined by bindingRegion). Otherwise, it will report the closest enhancer regions in one direction.
bindingRegion	Annotation range used together with bindingType, which is a vector with two integer values, default to c (-5000, 5000). The first one must be no bigger than 0. And the sec ond one must be no less than 1. For details, see bindingType.
ignore.peak.strand	ignore the peaks strand or not.
...	Not used.

Value

Output is a GRanges object of the annotated peaks.

Author(s)

Jianhong Ou

See Also

See Also as annotatePeakInBatch

Examples

  bed <- system.file("extdata", 
                     "wgEncodeUmassDekker5CGm12878PkV2.bed.gz",
                     package="ChIPpeakAnno")
  DNAinteractiveData <- toGRanges(gzfile(bed))
  library(EnsDb.Hsapiens.v75)
  annoData <- toGRanges(EnsDb.Hsapiens.v75, feature="gene")
  data("myPeakList")
  findEnhancers(myPeakList[500:1000], annoData, DNAinteractiveData)
  

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.