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!
