Question: Help with DiffBind plotVenn and referencing peak sets in general
gravatar for neumann.sylvia
11 weeks ago by
neumann.sylvia0 wrote:


I have ChIP peaksets for three different factors in two different treatment groups. For each I have several replicates.

I have generated a consensus peak set using:

consensus<-dba.peakset(dba, consensus=c(DBAFACTOR,DBACONDITION,DBA_TREATMENT), minOverlap=0.99)

Now I would like to plot the overlap between the consensus for FACTOR1 and TREATMENT1 and the individual replicate of FACTOR1 and TREATMENT2. How would I reference this?

I have tried many different ways to reference to the peaksets using the masks, but each time I run into errors. I guess my main question is how to reference different peaksets. Is there something simple like referencing the peak sets directly e.g:

dba.plotVenn(dba, dba$peaks[[1]] & dba$peaks[[2]])?

I am relatively new to R and I find it difficult to understand how the referencing works.

My dba looks like this and I want to generate a venn diagram between peakset [[26]] and peakset [[7]] for example:

31 Samples, 127175 sites in matrix (164664 total): ID Factor Condition Treatment Replicate Caller Intervals 1 SN009.BIC.CRTC1 CRTC1 No BIC 1 MACS2 114188 2 SN018.BIC.CRTC1 CRTC1 No BIC 2 MACS2 70108 3 SN025.BIC.CRTC1 CRTC1 No BIC 3 MACS2 75022 4 SN031.BIC1.CRTC1 CRTC1 No BIC 4 MACS2 94957 5 SN031.BIC2.CRTC1 CRTC1 No BIC 5 MACS2 79166 6 SN031.BIC3.CRTC1 CRTC1 No BIC 6 MACS2 90218 7 SN025.TTX.CRTC1 CRTC1 No TTX 1 MACS2 4925 8 SN031.TTX1.CRTC1 CRTC1 No TTX 2 MACS2 6097 9 SN031.TTX2.CRTC1 CRTC1 No TTX 3 MACS2 2719 10 SN031.TTX3.CRTC1 CRTC1 No TTX 4 MACS2 22379 11 SN009.BIC.CREB CREB No BIC 1 MACS2 99016 12 SN018.BIC.CREB CREB No BIC 2 MACS2 63697 13 SN025.BIC.CREB CREB No BIC 3 MACS2 86943 14 SN031.BIC1.CREB CREB No BIC 4 MACS2 110506 15 SN031.BIC2.CREB CREB No BIC 5 MACS2 85390 16 SN031.BIC3.CREB CREB No BIC 6 MACS2 98732 17 SN025.TTX.CREB CREB No TTX 1 MACS2 92764 18 SN031.TTX1.CREB CREB No TTX 2 MACS2 92971 19 SN031.TTX2.CREB CREB No TTX 3 MACS2 71877 20 SN031.TTX3.CREB CREB No TTX 4 MACS2 90041 21 SN031.TTX1.H3K4me3 H3K4me3 No TTX 1 MACS2 18638 22 SN031.TTX2.H3K4me3 H3K4me3 No TTX 2 MACS2 21175 23 SN031.TTX3.H3K4me3 H3K4me3 No TTX 3 MACS2 19710 24 SN031.BIC1.H3K4me3 H3K4me3 No BIC 1 MACS2 25221 25 SN031.BIC2.H3K4me3 H3K4me3 No BIC 2 MACS2 22059 26 CRTC1:BIC CRTC1 No BIC 1-2-3-4-5-6 MACS2 42780 27 CRTC1:TTX CRTC1 No TTX 1-2-3-4 MACS2 1062 28 CREB:BIC CREB No BIC 1-2-3-4-5-6 MACS2 45911 29 CREB:TTX CREB No TTX 1-2-3-4 MACS2 44805 30 H3K4me3:TTX H3K4me3 No TTX 1-2-3 MACS2 14807 31 H3K4me3:BIC H3K4me3 No BIC 1-2 MACS2 18091

Thanks, Sylvia

ADD COMMENTlink modified 9 weeks ago by Rory Stark3.0k • written 11 weeks ago by neumann.sylvia0
Answer: Help with DiffBind plotVenn and referencing peak sets in general
gravatar for Rory Stark
9 weeks ago by
Rory Stark3.0k
CRUK, Cambridge, UK
Rory Stark3.0k wrote:

Yes, you can directly specify the peaksets you want to include in the Venn diagram using the mask parameter as described in the help page for dba.plotVenn().

For example, you can just say:

dba.plotVenn(consensus, mask=c(7,26))
ADD COMMENTlink written 9 weeks ago by Rory Stark3.0k
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