ChIPpeakAnno (version 3.6.5)

IDRfilter: Filter peaks by IDR (irreproducible discovery rate)

Description

Using IDR to assess the consistency of replicate experiments and obtain a high-confidence single set of peaks

Usage

IDRfilter(peaksA, peaksB, bamfileA, bamfileB,  maxgap=0L, minoverlap=1L, singleEnd=TRUE, IDRcutoff=0.01, ...)

Arguments

peaksA, peaksB

peaklist, GRanges object.

bamfileA, bamfileB

file path of bam files.

maxgap

Non-negative integer. Peak intervals with a separation of maxgap or less are considered to be overlapped.

minoverlap

Non-negative integer. Peak intervals with an overlapping of minoverlap or more are considered to be overlapped.

singleEnd

(Default TRUE) A logical indicating if reads are single or paired-end.

IDRcutoff

If the IDR no less than IDRcutoff, the peak will be removed.

...

Not used.

Value

An object GRanges

References

Li, Qunhua, et al. "Measuring reproducibility of high-throughput experiments." The annals of applied statistics (2011): 1752-1779.

Examples

  if(interactive()){
    library(MMDiffBamSubset)
    peaksA=toGRanges(WT.AB2.Peaks(), format="MACS")
    peaksB=toGRanges(Resc.AB2.Peaks(), format="MACS")
    bamfileA=WT.AB2()
    bamfileB=Resc.AB2()
    IDRfilter(peaksA, peaksB,
              bamfileA, bamfileB)
  }