Collapse core regions from a BED file with score-based filtering

This function reads a BED file, filters regions by score, resizes them to a fixed core width, and merges overlapping cores selectively based on score differences. It supports chromosome-wise parallel processing and optional output to a BED file with logging throughout.

Usage

plc_coreovl_with_d(
  bed_file,
  score_threshold = 0.75,
  score_diff = 0.1,
  core_width = 151,
  return_gr = TRUE,
  output_dir = NULL,
  save_rds = FALSE,
  num_cores = NULL,
  processing_method = "multisession"
)

Arguments

bed_file

Path to the input BED file.

score_threshold

Numeric threshold for filtering regions by score from 0-1. Default is 0.75.

score_diff

Maximum allowed score difference between overlapping regions for merging. Default is 0.1.

core_width

Width to which each region should be resized (centered). Default is 151.

return_gr

Logical. If TRUE, returns the final collapsed GRanges object. Default is TRUE.

output_dir

Optional directory path to write BED output. If NULL, no output is written.

num_cores

Number of CPU cores to use. If NULL, will use half of available cores (up to 25). Default is NULL.

Value

If `return_gr = TRUE`, returns a `GRanges` object containing the collapsed regions. Otherwise, returns `NULL`.

Details

The function performs the following steps:

1. Loads and filters BED entries by score.

2. Resizes regions to a fixed core width centered on each region.

3. Merges overlapping cores selectively per chromosome using a parallel backend.

4. Logs progress and optionally writes output to BED format.

If no regions pass the score filter, the function exits early with a warning.