Enhancement: Promoters Calculated Don't Overlap with Other Genes

[DarioS]

I am trying to reproduce a published study by reimplementing the algorithm. The algorithm takes 200000 bases, the average length of a Topologically Associated Domain (TAD), upstream of the TSS and downstream of the TES. GenomicRanges has a function named promoters. It would be nice to have a setting such as nonOverlapping = TRUE that would extend the promoter region upstream until it reaches another gene's exon in the GRangesList object or 200000 bases, whichever is lesser.

[m-swirski]

Hi, it should easily be done by a combination of precede, distance, and promoters functions, as promoters accept full vector of values. If you want I can show you how to get it done. BTW. for processing of granges list I would recommend using ORFik package:
https://github.com/Roleren/ORFik

Genomic Ranges promoters function doesn't retain exon structure.

[DarioS]

Thanks. I got it done using promoters and setdiff.

[lshep]

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