Question

Dba.Peakset does not work

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fusion.slope ▴ 10

@fusionslope-12296

Last seen 6.1 years ago

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

diffbind dba.peakset • 1.1k views

ADD COMMENT • link updated 7.9 years ago by Rory Stark ★ 5.2k • written 7.9 years ago by fusion.slope ▴ 10

score 2 · Accepted Answer · 2017-02-07

As you can see, the DBA object mESC contains only one peakset. This is because you aren't passing in mESC to subsequent calls to dba.peakset() after the first call (repeating NULL instead). Your code should look like:

> 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(mESC,
                      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(mESC,
                      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

Cheers-

Rory