Wondering if the basic matrix output from dba.count in DiffBind would be an appropriate input matrix into DESeq2 (via DESeqDataSetFromMatrix) or if has to be modified in some other fashion? I want to run DESeq2 interactions on this interval read count matrix generated by DiffBind. Thank you.
Yes this can be used to create a DESeqDataSet object. You have to pay attention to the score, which should be DBA_SCORE_READS (or, more controversially, DBA_SCORE_READ_MINUS). You can change an existing score without recounting by calling dba.count() with peaks=NULL, then retrieve the counts using dba.peakset():
> myDBA <- dba.count(myDBA, peaks=NULL, score=DBA_SCORE_COUNTS)
> rangedCounts <- dba.peakset(myDBA, bRetrieve=TRUE)If you want the counts by themselves (without the site interval ranges) in a matrix (for use in DESeqDataSetFromMatrix) :
> counts <- as.matrix(mcols(rangedCounts))
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version 2.3.6
Thanks for the info Rory! Thats pretty much what I have been doing. Is there a good way on the back end, once I do whatever interaction analysis with DESeq2, to quickly interrogate specific intervals (differential/interacting ones I find interesting) when the site interval ranges are removed from the matrix I am inputting into DESeqDataSet?
I guess with genes and transcripts its easier since you have the identifier/name. I guess they still have the first numbered column of the matrix.
Wondering if its possible to return the dba.peakset as a RangedSummarizedExperiment object?