peaksNearBDP: obtain the peaks near bi-directional promoters

Description

Obtain the peaks near bi-directional promoters. Also output percent of peaks near bi-directional promoters.

Usage

peaksNearBDP(myPeakList, AnnotationData, MaxDistance=5000L, ...)

Arguments

myPeakList

GRanges or RangedData: See example below

AnnotationData

annotation data obtained from getAnnotation or customized annotation of class GRanges containing additional variable: strand (1 or + for plus strand and -1 or - for minus strand). For example, data(TSS.human.NCBI36), data(TSS.mouse.NCBIM37), data(TSS.rat.RGSC3.4) and data(TSS.zebrafish.Zv8).

MaxDistance

Specify the maximum gap allowed between the peak and nearest gene

...

Not used

Value

A list of 4
peaksWithBDPannotated Peaks containing bi-directional promoters.
GRangesList with slot start holding the start position of the peak, slot end holding the end position of the peak, slot space holding the chromosome location where the peak is located, slot rownames holding the id of the peak. In addition, the following variables are included.
feature: id of the feature such as ensembl gene ID
insideFeature: upstream: peak resides upstream of the feature; downstream: peak resides downstream of the feature; inside: peak resides inside the feature; overlapStart: peak overlaps with the start of the feature; overlapEnd: peak overlaps with the end of the feature; includeFeature: peak include the feature entirely.
distancetoFeature: distance to the nearest feature such as transcription start site. By default, the distance is calculated as the distance between the start of the binding site and the TSS that is the gene start for genes located on the forward strand and the gene end for genes located on the reverse strand. The user can specify the location of peak and location of feature for calculating this
feature_range: start and end position of the feature such as gene
feature_strand: 1 or + for positive strand and -1 or - for negative strand where the feature is located
percentPeaksWithBDPThe percent of input peaks containing bi-directional promoters
n.peaksThe total number of input peaks
n.peaksWithBDPThe # of input peaks containing bi-directional promoters

References

Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237

Examples

Run this code

if (interactive())
{
    data(myPeakList)
    data(TSS.human.NCBI36)
    annotatedBDP = peaksNearBDP(myPeakList[1:6,], 
                                AnnotationData=TSS.human.NCBI36,
                                MaxDistance=5000,
                                PeakLocForDistance =  "middle", 
                                FeatureLocForDistance = "TSS")
    c(annotatedBDP$percentPeaksWithBDP, annotatedBDP$n.peaks, 
      annotatedBDP$n.peaksWithBDP)
}