Cfp1-Peaks: Peaks for Cfp1-data set

In dhelekal/mmdiff3: Statistical Testing for ChIP-Seq data sets

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)

dhelekal/mmdiff3 documentation built on July 25, 2019, 8:18 p.m.