Hello,
am trying to import bed files from MACS2 peak calling with dba.peakset function. I have 3 files and i would like to import in this way:
mESC <- dba.peakset(NULL,peaks="/home/tandrean/Desktop/Gadd45-TKO/4.test_peaks.narrowPeak",
peak.caller="bed", peak.format= "narrow",sampID="Gadd45.TKO.1",tissue="mESC",
factor="ER",condition="TKO",replicate=1)
mESC <- dba.peakset(NULL,
peaks="/home/tandrean/Desktop/Gadd45-TKO/5.test_peaks.narrowPeak",
peak.caller="bed", peak.format= "narrow", sampID="Gadd45.TKO.2",tissue="mESC",
factor="ER",condition="TKO",replicate=2)
mESC <- dba.peakset(NULL,
peaks="/home/tandrean/Desktop/Gadd45-TKO/6.test_peaks.narrowPeak",
peak.caller="bed", peak.format= "narrow", sampID="Gadd45.TKO.3",tissue="mESC",
factor="ER",condition="TKO",replicate=3)
mESC
output:
1 Samples, 40377 sites in matrix: ID Tissue Factor Condition Treatment Replicate Caller Intervals 1 Gadd45.TKO.3 mESC ER TKO 3 bed 40377 |
Now i would like to merge the peak with dba.peakset like this:
mESC.consensus <- dba.peakset(mESC,1:3, minOverlap=3, bRetrieve=TRUE)
I have an error at this step: Error in pv$peaks[[i]] : subscript out of bounds
Any Help? What am I doing wrong? Thanks |