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Create list of poly(A) tail chunks centered on significant signal deviations

Source: R/ninetails_core_functions.R
create_tail_chunk_list.Rd

Extracts fragments of poly(A) tails of ONT RNA reads potentially containing non-A nucleotides, along with their coordinates, and appends the data to a nested list organized by read IDs.

Usage

create_tail_chunk_list(tail_feature_list, num_cores)

Arguments

tail_feature_list

List object produced by create_tail_feature_list.

num_cores

Numeric. Number of physical cores to use in processing. Do not exceed 1 less than the number of cores at your disposal.

Value

A nested list containing the segmented tail data (chunks and coordinates) organized by read IDs. Each read entry contains one or more fragments, where each fragment is a list with:

chunk_sequence

Numeric vector. Raw signal values (length 100)

chunk_start_pos

Integer. Starting index of the chunk in the original signal

chunk_end_pos

Integer. Ending index of the chunk in the original signal

Details

Parallelization is handled with foreach and doSNOW. A progress bar is displayed during processing. After extraction, empty list elements are pruned and chunk moves are dropped to minimize memory footprint.

See also

create_tail_feature_list for preparing the input, split_tail_centered for the per-read segmentation logic, create_gaf_list for downstream GAF transformation

Examples

if (FALSE) { # \dontrun{

tcl <- ninetails::create_tail_chunk_list(
  tail_feature_list = tfl,
  num_cores = 3
)

} # }