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Merge polyA and polyT processing results for cDNA analysis

Source: R/ninetails_core_functions_dorado_cDNA.R
merge_cdna_results.Rd

This function combines the results from separate polyA and polyT processing paths into a unified output in standard ninetails format. Updated to work with the simplified approach using tibbles instead of files.

Usage

merge_cdna_results(
  polya_results = NULL,
  polyt_results = NULL,
  unidentified_reads = NULL,
  save_dir,
  prefix = "",
  cli_log = message
)

Arguments

polya_results

List. Results from polyA processing (from process_polya_reads_cdna). Can be NULL if no polyA reads were found.

polyt_results

List. Results from polyT processing (from process_polyt_reads_cdna). Can be NULL if no polyT reads were found.

unidentified_reads

Data frame/tibble. Reads that could not be classified as polyA or polyT (with tail_type = "unidentified").

save_dir

Character. Directory where merged results will be saved.

prefix

Character. Optional prefix for output file names.

cli_log

Function for logging messages and progress.

Value

List containing merged cDNA results in standard ninetails format:

read_classes

Data frame with all read classifications including tail_type

nonadenosine_residues

Data frame with all predicted modifications including tail_type

Examples

if (FALSE) { # \dontrun{
merged_results <- merge_cdna_results(
  polya_results = polya_output,
  polyt_results = polyt_output,
  unidentified_reads = unidentified_tibble,
  save_dir = "path/to/output/",
  prefix = "experiment1",
  cli_log = message
)
} # }