GoekeLab/proActiv

optimize preparation of promoter annotation object

Closed this issue · 1 comments

jleechung commented
  • improve runtime for preparing promoter annotation from a transcript database (currently takes ~1 hr on Windows OS without parallelization)
jleechung commented
  • promoter annotation helper code optimized at two bottlenecks:
    • replace lapply in calculating reduced exon ranges with dplyr pipe (annotation-data-helper.R, getReducedExonRanges)
    • replace lapply in calculating intron ranks with dplyr pipe (annotation-data-helper.R, getIntronRanks)
  • restructure promoter annotation code to remove duplicate calls