Read in a BEDPE file and convert it to a GInteractions object with refactored seq details. Flexible to different naming conventions but expects the 6 columns for breakpoint chr1, start1, end1, and breakpoint chr2, start2, end2. Can also return data.table or GRangesList for convenience.
Usage
read_bedpe_file(
bedpe_file,
output_type = c("gi", "dt", "grl"),
keep_metadata = TRUE,
verbose = TRUE
)Arguments
- bedpe_file
Path to BEDPE file or data.table/data.frame
- output_type
Character string specifying output format: gi="GInteractions" (default), dt="data.table", or grl="GRangesList"
- keep_metadata
Logical, whether to preserve metadata (default: TRUE)
- verbose
Logical, whether to print progress messages. (default: TRUE)