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

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()){
    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)
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/IDRfilter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IDRfilter
> ### Title: Filter peaks by IDR (irreproducible discovery rate)
> ### Aliases: IDRfilter
> ### Keywords: misc
> 
> ### ** Examples
> 
> #  if(interactive()){
>     library(MMDiffBamSubset)
>     peaksA=toGRanges(WT.AB2.Peaks(), format="MACS")
duplicated or NA names found. Rename all the names by numbers.
>     peaksB=toGRanges(Resc.AB2.Peaks(), format="MACS")
duplicated or NA names found. Rename all the names by numbers.
>     bamfileA=WT.AB2()
>     bamfileB=Resc.AB2()
>     IDRfilter(peaksA, peaksB,
+               bamfileA, bamfileB)
GRanges object with 3307 ranges and 1 metadata column:
          seqnames               ranges strand |
             <Rle>            <IRanges>  <Rle> |
  olp0001     chr1   [3140628, 3141907]      * |
  olp0002     chr1   [3143686, 3144714]      * |
  olp0003     chr1   [3334413, 3335494]      * |
  olp0004     chr1   [3471587, 3474399]      * |
  olp0005     chr1   [3659128, 3661641]      * |
      ...      ...                  ...    ... .
  olp3303    chr10 [26653593, 26654982]      * |
  olp3304    chr10 [26974273, 26975788]      * |
  olp3305    chr10 [27079188, 27080561]      * |
  olp3306    chr10 [27335950, 27337151]      * |
  olp3307    chr10 [27537860, 27546476]      * |
                                          peakNames
                                    <CharacterList>
  olp0001               peaksB__X0001,peaksA__X0003
  olp0002               peaksB__X0002,peaksA__X0004
  olp0003               peaksB__X0003,peaksA__X0006
  olp0004 peaksB__X0004,peaksA__X0007,peaksA__X0008
  olp0005               peaksA__X0010,peaksB__X0007
      ...                                       ...
  olp3303               peaksA__X4457,peaksB__X4970
  olp3304               peaksB__X4972,peaksA__X4458
  olp3305               peaksA__X4459,peaksB__X4973
  olp3306               peaksB__X4974,peaksA__X4460
  olp3307               peaksA__X4462,peaksB__X4976
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>