Hi,

I was following the SGSeq tutorial, but there were some things that I didn't understand properly. I would appreciate further explanation, please.

As following the tutorial document of SGSeq for section 11, I created the SGVariantCounts object:

sgv <- rowRanges(sgvc_pred)
sgvc <- getSGVariantCounts(sgv, sample_info = si)
sgvc


x <- counts(sgvc)
vid <- variantID(sgvc)
> vid
[1] 1 2
# vid output is only an integer. Could you explain what these numbers are? as well as for eid?

eid <- eventID(sgvc)
> eid
[1] 1 1

Then, the plan was to use DEXSeq for differential splice variant usage.

What information do I have to extract and use as input for differential splicing analysis using DEXSeq? How do I build my DEXSeqDataSet object for further analysis?

In the documentation of DEXSeq they used DEXSeqDataSetFromSE to build DEXSeqDataSet object as follow:

dxd = DEXSeqDataSetFromSE( se, design= ~ sample + exon + condition:exon )

Now, as I used SGSeq; what do I have to use to create the DEXSeqDataSet object? Should I use the DEXSeqDataSetFromSE function, and replace see with x which is the counts(sgvc)? or there is another way? How I have to make my design? use vid from SGSeq instead of exon in the dxd from DEXSeq?

I suppose I have to use my SGVariantCounts objects in my SGSeq output as an input in DEXseq like this, but I am not sure:

dxd = DEXSeqDataSet(countData = x, featureID = vid, groupID = eid, design=  ~ sample + exon + condition:exon)

but then here how to define sample and exon?! or where to get these info from my SGSeq analysis?

I would appreciate any help!

Many thanks in advance!