findEnhancers {ChIPpeakAnno} | R Documentation |
Find possible enhancers by data from chromosome conformation capture techniques such as 3C, 5C or HiC.
findEnhancers( peaks, annoData, DNAinteractiveData, bindingType = c("nearestBiDirectionalPromoters", "startSite", "endSite"), bindingRegion = c(-5000, 5000), ignore.peak.strand = TRUE, ... )
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.
|
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. |
Output is a GRanges object of the annotated peaks.
Jianhong Ou
See Also as annotatePeakInBatch
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)