Hi!
I would like to generate a cosplicing network similar to how it's described here (https://github.com/iancuo/cosplicingNetworks). My understanding is that I would need normalized exon/transcript counts prior to generating the network. For DEXSeq, I was planning to input the normalized exon counts from the DEXSEqDataSet generated as follows:
dxd <- DEXSeqDataSet(countData=count.data, sampleData=sample.data, design=~sample + exon + group:exon, featureID=counts(d)$featureid, groupID=counts(d)$geneid)
system.time({ dxd <- estimateSizeFactors(dxd) dxd <- estimateDispersions(dxd, quiet=TRUE) dxd <- nbinomLRT(dxd, reduced=~sample + exon) })
dxd_norm<-counts(dxd,normalized=T)
I was wondering whether a similar option is available to output normalized transcript levels from DRIMSeq?
Thanks!
Maya
Ah, ok - that makes sense! Thanks!!