Differential ChIP regions across >2 conditions
0
0
Entering edit mode
Shamaine • 0
@shamaine-15636
Last seen 5.5 years ago

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.

diffbind chipseq • 744 views
ADD COMMENT

Login before adding your answer.

Traffic: 832 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6