Question: Structure of DiffBind dba.count matrix equivalent to DESeqDataSetFromMatrix input?
gravatar for rbronste
11 months ago by
rbronste60 wrote:

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.

ADD COMMENTlink modified 11 months ago by Rory Stark2.6k • written 11 months ago by rbronste60
gravatar for Rory Stark
11 months ago by
Rory Stark2.6k
CRUK, Cambridge, UK
Rory Stark2.6k wrote:

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))


ADD COMMENTlink written 11 months ago by Rory Stark2.6k

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.

ADD REPLYlink written 11 months ago by rbronste60

Wondering if its possible to return the dba.peakset as a RangedSummarizedExperiment object?

ADD REPLYlink written 10 months ago by rbronste60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 158 users visited in the last hour