After running tximeta, the SummarizedExperiment output
will have GRanges representing the transcript locations
attached as rowRanges to the object. These provide the
start and end of the transcript in the genomic coordiantes, and
strand information. However, the exonic locations are not provided.
This function, addExons, swaps out the GRanges
with a GRangesList, essentially a list along the rows of the
SummarizedExperiment, where each element of the list is a
GRanges providing the locations of the exons for that transcript.
addExons(se)a SummarizedExperiment
This function is designed only for transcript-level objects.
This "lack of a feature" reflects a belief on the part of the package author
that it makes more sense to think about exons belonging to transcripts
than to genes. For users desiring exonic information alongside
gene-level objects, for example, which exons are associated with
a particular gene, it is recommended to pull out the relevant
GRangesList for the transcripts of this gene, while the object
represents transcript-level data, such that the exons are still
associated with transcripts.
For an example of addExons, please see the tximeta vignette.