Create Ninetails output tables for Dorado cDNA pipeline

This function extends create_outputs_dorado to handle cDNA data with additional tail_type information. It produces the same output structure as the DRS pipeline but preserves the tail_type column for read orientation information.

Usage

create_outputs_dorado_cdna(
  dorado_summary_dir,
  nonA_temp_dir,
  polya_chunks_dir,
  num_cores = 1,
  qc = TRUE
)

Arguments

dorado_summary_dir

Character string. Path to a directory containing Dorado summary files (.txt, .tsv, or .csv) with per-read poly(A) tail information and tail_type.

nonA_temp_dir

Character string. Path to a directory containing non-adenosine prediction RDS files, generated from temporary models.

polya_chunks_dir

Character string. Path to a directory containing poly(A) chunk RDS files used for position inference of predictions.

num_cores

Integer. Number of cores to use for parallelized file loading and processing. Must be a positive integer. Default is 1.

qc

Logical. Whether to apply quality control filtering of terminal predictions (removing predictions near the ends of poly(A) tails). Default is TRUE.

Value

A named list with two data frames (identical to DRS output + tail_type):

read_classes

Data frame with per-read classification results, including columns for read name, contig, poly(A) length, QC tag, class, comments, and tail_type.

nonadenosine_residues

Data frame with per-chunk predictions of non-adenosine residues, including read name, contig, predicted base, estimated position within the poly(A) tail, poly(A) length, QC tag, and tail_type.

Examples

if (FALSE) { # \dontrun{
results <- create_outputs_dorado_cdna(
dorado_summary_dir = "data/dorado_summaries",
nonA_temp_dir = "data/nonA_predictions",
polya_chunks_dir = "data/polya_chunks",
num_cores = 4,
qc = TRUE
)

# Access read classifications with tail_type
head(results$read_classes)

# Access non-adenosine residues with tail_type
head(results$nonadenosine_residues)
} # }