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ashakru / BilbORF

R package for performing differential ORF usage analysis
MIT License
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`annotate_orfs_isoforms` to perform automatic Kozak sequence score calculation #7

Open ashakru opened 12 months ago

ashakru commented 12 months ago

Add a column to the table output of annotate_orf_isoforms with the Kozak sequence score computed. Likely to use ORFik::kozakSequenceScore

ashakru commented 12 months ago

Currently there is a problem with setting appropriate input for ORFik::kozakSequenceScore. The error is:

Error in pmapToTranscriptF(grl, reference, ignore.strand = ignore.strand,  : 
  subscript contains out-of-bounds indices

And it comes from startRegion() and further windowPerGroup() function. I tried to play with setting names within the GRangesLists with ORFs and respective transcripts coordinates, but it didn't work.