Hi Rory, Thanks and sorry about commenting instead of starting a new question. I have copy-pasted the question below for reference , and would like to follow up on your response.

I may have to rephrase my question: Beyond visualization, I wanted to know if it is possible for DiffBind to identify differential peaks across all 4 different conditions. Currently, when we set a dba.contrast(), it only compares between 2 groups at a time. 

Thank you! 

Original Question and Response:

Dear Rory,

I am a beginner to bioinformatics and DiffBind. Firstly, thank you for this very useful tool and the handy guides! I have some additional questions regarding using DiffBind on more than 2 conditions.

Currently I have 4 different conditions (representing different "subtypes" of a disease condition) and would like to identify differential peaks among all 4 different conditions (ideally identify peaks that are specific to each subtype).

I have set up all possible contrasts (i.e. 6 different contrasts). However from what I know, DiffBind only allows identification of differential regions between 2 conditions. As a result, for heatmap visualization of differential peak regions , at any one point I can only visualize one contrast that clusters the 2 conditions in that contrast. 

I am not sure if it is possible to use DiffBind to obtain a heatmap plot that can ideally cluster the 4 different conditions according to differential peak regions across all 4 conditions?

Please correct me if I have any misunderstanding. 

Thank you!

Best regards,
Shamaine 

---

Given a set of DB sites from a contrast, you can see how all the samples cluster, whether or not they are in the contrast, by setting the mask parameter to eg dba.plotHeatmap() and dba.plotPCA(). So if you have 4 conditions and 3 replicates of each, you can set mask=1:12 and all the samples will be plotted using the DB sites from the specified contrast.