Dear All,

I am analyzing ChIP-seq data where I have multiple groups. I am interested in getting differential binding across complex contrasts like:

((condition1 vs. condition2) vs. (condition3 vs. condition4))

I am unable to figure out how to provide such complex contrast to the dba.contrast function in the DiffBind R package. If somebody has worked on such a study kindly share your solution with me.

Thanking you in advance!

Note: That's how my condition column looks like:

metadata$Condition
 [1] 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3 4 4 4 4 4 4 4
Levels: 1 2 3 4

and that's how I am calling the dba.contrast function:

DAPs <- dba.contrast(DAPs, categories=DBA_CONDITION)

As per my understanding by following this rationale, I can get simpler contrast e.g. condition1 - condition2 by the call like:

DAPs.DB <- dba.report(DAPs, 1, method=DBA_EDGER, DataType=DBA_DATA_FRAME, th=0.05, bUsePval=TRUE, bCalled=TRUE)

or condition3 - condition4 by the call like:

DAPs.DB <- dba.report(DAPs, 2, method=DBA_EDGER, DataType=DBA_DATA_FRAME, th=0.05, bUsePval=TRUE, bCalled=TRUE)