The current DEXSeq manual suggests using:
exonicParts = exonicParts( txdb, linked.to.single.gene.only = TRUE )
To generate an "exonic parts" feature set (GRanges object).
However, the current
exonicParts call in GenomicFeatures omits a step, that was previously present for
disjointExons, that determined and added the
exonic_part information to the metadata of the final object.
Thus following the manual in DEXSeq using the R-centric commands does not work and results in an error:
Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) : make sure your SummarizedExperiment object contain the columns geneid, txname and exonic_part