Hi,

I am using the R package, Genomic Features, to get Intron Expression and
the function that I am using is the intronsByTranscript(). While this
function is useful, it returns the number of raw reads that align to each
intron grouped at the transcript level. Is there an easy way to get it to
group it by a gene such that I am grabbing all the introns that fall in all
the transcripts belong to a gene (and without double counting the intronic
space).

Similar, is there a way to easily get the raw read count at an individual
intron level rather than having it grouped? The introns() function seems to
be defunct now as it recommends that we use the intronsByTranscript()
function.

Thanks,

Fong

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