Cfp1-Peaks {MMDiff2} | R Documentation

## Peaks for Cfp1-data set

### Description

Subset of MACS called Peaks for Cfp-1 data set. Consensus Peaks were created using diffBind (see below).

### Usage

    data('Cfp1-Peaks')

### Format

contains Peaks, a GRanges object with 500 ranges and 3 metadata columns

### References

data taken from Clouaire et al., Genes and Development, 2012.

### Examples

    # data was created as follows:
    ## Not run:
    library('MMDiffBamSubset')
    dataDir <- system.file("extdata", package="MMDiffBamSubset")
    library('DiffBind')
    olddir <- setwd(dataDir)
    DBA <- dba(sampleSheet="Cfp1.csv", minOverlap=3)
    Peaks <- dba.peakset(DBA, bRetrieve = TRUE)
    DBA <- dba.count(DBA, minOverlap=3)
    setwd(olddir)
    peaks <- dba.peakset(DBA, bRetrieve=TRUE)
    C <- Counts(MMD)
    idx <- which(C[,1]>150 & C[,3]>150&width(Peaks)>1000&width(Peaks)<5000)
    Peaks <- Peaks[idx[1:500]]

    ## End(Not run)

[Package MMDiff2 version 1.20.0 Index]