make_junction_ab — make_junction

This function processes STARsolo splicing junction output to create a modality list for splicing data. It supports both single and multiple sample processing, optional barcode filtration, and internal whitelist usage.

Usage

make_junction_ab(
  STARsolo_SJ_dirs,
  white_barcode_lists = NULL,
  sample_ids,
  use_internal_whitelist = TRUE,
  verbose = FALSE,
  keep_multi_mapped_junctions = FALSE,
  ...
)

Arguments

STARsolo_SJ_dirs: A character vector or list of strings representing the paths to STARsolo SJ directories. Each directory should contain the raw splicing junction output files.
white_barcode_lists: A list of character vectors, each containing barcode whitelist(s) for the corresponding sample. If NULL (default), the function uses the internal STARsolo whitelist if use_internal_whitelist is TRUE.
sample_ids: A character vector or list of unique sample IDs corresponding to each directory in STARsolo_SJ_dirs.
use_internal_whitelist: A logical flag (default TRUE) indicating whether to use the internal STARsolo whitelist located at ../Gene/filtered/barcodes.tsv for each sample when white_barcode_lists is NULL.
verbose: Logical (default FALSE). If TRUE, prints detailed progress messages during processing.
keep_multi_mapped_junctions: Logical (default FALSE). If TRUE, retains multi-mapped junctions (flag 0). If FALSE, only keeps uniquely mapped junctions (flag 1).
...: Additional parameters for future extensions.

Value

A list containing processed splicing modality data for each sample. If a single sample is provided, the function returns the processed data as a list. For multiple samples, a named list is returned. Each sample's result contains:

eventdata: A data.table containing feature metadata.
junction_ab: A sparse matrix of junction abundance.