I have a table of results from DEXSeq, but don't have the row data. I would like to plot some genes, using your plotDEXSeq function, but if I simply enter the dataframe I have, it returns an error
plotDEXSeq(DF, "Jak2", displayTranscripts=TRUE, legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )
Error in plotDEXSeq(as.matrix(DF), "Jak2", displayTranscripts = TRUE, : is(object, "DEXSeqResults") | is(object, "DEXSeqDataSet") is not TRUE
I'd be happy to run DEXSeq from the information I have in the table.
dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile )
I imagine there is a way as I have the counts. Something equivalent to DESeqDataSetFromMatrix. But I can't make it work. Here are the column contained in the table:
row names are groupID:featureID
Is there a way to exploit this? Thank you for your help