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personal scripts for common bioinformatic pipelines
When running the summariseOverlaps()
function an error occurs:
Error in registered()[[bpparamClass]] :
attempt to select less than one element in get1index
This seems to come from BiocParallel
, but I could not understand the problem so far...
At the moment TPM and FPKM are estimated based on the gene length calculated as the start to end distance. However, this is unfair, as some genes might have much bigger introns than others.
Therefore the counts should be scaled to the length of union of exons instead.
Something like this snippet of code might work:
exons <- exonsBy(annotation, by="gene")
# ... rest of the code with summariseOverlaps
# and then
exons_reduced <- reduce(exons)
exons_lengths <- sum(width(exons_reduced))
exonsdf <- unlist(exons_reduced)
# or something like that
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