IDRfilter: Filter peaks by IDR (irreproducible discovery rate)

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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 = -1L,
  minoverlap = 0L,
  singleEnd = TRUE,
  IDRcutoff = 0.01,
  ...
)

Arguments

peaksA, peaksB	peaklist, GRanges object.
bamfileA, bamfileB	file path of bam files.
maxgap, minoverlap	Used in the internal call to findOverlaps() to detect overlaps. See ?findOverlaps in the IRanges package for a description of these arguments.
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

Author(s)

Jianhong Ou

References

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

Examples

  if(interactive()){
    path <- system.file("extdata", "reads", package="MMDiffBamSubset")
    if(file.exists(path)){
            bamfileA <- file.path(path, "reads", "WT_2.bam")
            bamfileB <- file.path(path, "reads", "Resc_2.bam")
            WT.AB2.Peaks <- file.path(path, "peaks", "WT_2_Macs_peaks.xls")
            Resc.AB2.Peaks <- file.path(path, "peaks",
                                       "Resc_2_Macs_peaks.xls")
            peaksA=toGRanges(WT.AB2.Peaks, format="MACS")
            peaksB=toGRanges(Resc.AB2.Peaks, format="MACS")
            library(idr)
            library(DelayedArray)
            IDRfilter(peaksA, peaksB,
                        bamfileA, bamfileB)
    }
  }

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.