There are two ways to make vector of exon ranking: 1. Iterate per exon in ORF, byTranscript = FALSE 2. Iterate per ORF in transcript, byTranscript = TRUE.
logical (default: FALSE), groups orfs by transcript name or ORF name, if ORfs are by transcript, check duplicates.
Either by transcript or by original groupings. Must be ordered, so that same transcripts are ordered together.
an integer vector of indices for exon ranks
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