Description

Quantitative R-loop tracks present normalized and weighted R-loop signals integrated across multiple profiling technologies and biological samples, yielding both R-loop scores and R-loop zones. The R-loop score is displayed as three stacked bigWig tracks representing Watson-strand, Crick-strand, and undetermined-strand signals, together offering a genome-wide view of R-loop occupancy. R-loop zones are defined by trimming continuous signal tracts at 25% of their local maximum. This track provides a unified, normalized view of the R-loop landscape across diverse datasets, enabling users to identify conserved, high-confidence R-loop-forming loci.

Methods

• Data Preparation
  First, to eliminate the influence of inter-sample score differences, we applied a modified Robust Z-score to normalize the signal values of each sample to a comparable level. The Robust Z-score was calculated as (R-loop peak score - lower fence) / MAD, and values greater than 10 were capped, completing per-sample normalization.
• Calculation of technology score
  Second, to facilitate the summation of signals across samples, R-loop peak signals were assigned to 100-bp sliding windows with which they overlapped by =50 bp. The sliding window advanced in 10-bp steps, and the signals within each window were summed, yielding per-sample scores in contiguous 10-bp genomic windows. Within the same technology, each sample was given equal weight, and their window scores were directly summed to obtain a technology score. For stranded R-loop technologies, strand information was retained during computation to define the strandness of the final results; meanwhile, Watson and Crick peaks were merged for calculation to enable summation with non-stranded R-loop technologies.
• Calculation of R-loop score and R-loop zone
  When computing the R-loop score across all technologies, each technology was assigned equal weight and the scores were summed. The summed window score was further multiplied by the number of technologies with a score > 0 in that window to yield the non-stranded R-loop score. Contiguous regions with a score > 0 were trimmed by removing the portion below 25% of the maximum score within the region, producing non-stranded R-loop regions. The same procedure was applied to stranded R-loop technologies to obtain stranded R-loop score and stranded R-loop regions. Non-stranded R-loop score that overlapped with Watson or Crick R-loop scores were proportionally assigned to the Watson or Crick strand. Non-stranded R-loop regions, if overlapped with stranded R-loop regions, were also assigned to Watson or Crick R-loop zones accordingly. The remaining non-stranded R-loop score and regions were considered to have undetermined strandness.