Hello,

I`m trying to create an exon count object, there seems to be 2 ways

Using newExonCountSet, arguments needed include counts matrix, geneID,
exonID,transcriptID etc.

Using read.HTSeqCounts, arguments needed include filelist, annotation file
etc.

How can I use read.HTSeqCounts with the argument counts as input instead of
providing a file list? I already have a matrix of counts for each exon bin
(created by a combination of dexseq_count.py and  some processing on my
end) and a flattened annotation file (obtained from
dexseq_prepare_annotation.py).

I understand that I could use newExonCountSet instead, but extracting the
transcripts argument from the annotations file seems non-trivial, and I
want to detect differentially expressed transcripts an also plot them.

Please advise.

Thanks,
Al

	[[alternative HTML version deleted]]

