Filters out signals of a given nucleotide type for neural network training-set preparation.

Top-level convenience wrapper that orchestrates the complete training-set production pipeline for a single nucleotide category. Depending on the selected nucleotide, it chains the appropriate feature extraction, chunk splitting, filtering, and GAF creation functions into a single call.

Usage

prepare_trainingset(
  nucleotide,
  nanopolish,
  sequencing_summary,
  workspace,
  num_cores = 1,
  basecall_group = "Basecall_1D_000",
  pass_only = TRUE
)

Arguments

nucleotide

Character. One of "A", "C", "G", or "U". Defines the type of signal filtering applied to produce training data for the desired nucleotide context.

nanopolish

Character string. Full path of the .tsv file produced by nanopolish polya.

sequencing_summary

Character string. Full path of the .txt file with the sequencing summary.

workspace

Character string. Full path of the directory containing basecalled multi-Fast5 files.

num_cores

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

basecall_group

Character string ["Basecall_1D_000"]. Name of the level in the Fast5 file hierarchy from which the data should be extracted.

pass_only

Logical [TRUE]. If TRUE, only reads tagged by nanopolish as "PASS" are retained. Otherwise, reads tagged as "PASS" or "SUFFCLIP" are included.

Value

A named list of GAF matrices organised by <read_ID>_<index>. Always assign this returned list to a variable; printing the full list to the console may crash the R session.

Details

The internal pipeline differs by nucleotide:

"A"

Uses the A-only branch: create_tail_feature_list_A \(\rightarrow\) create_tail_chunk_list_A \(\rightarrow\) create_gaf_list_A.

"C"

Uses the non-A branch with value = -1 (valley filtering): create_tail_feature_list_trainingset \(\rightarrow\) create_tail_chunk_list_trainingset \(\rightarrow\) filter_nonA_chunks_trainingset \(\rightarrow\) create_gaf_list.

"G"

Uses the non-A branch with value = 1 (peak filtering).

"U"

Uses the non-A branch with value = -1 (valley filtering), same filter direction as C.

See also

create_tail_feature_list_trainingset, create_tail_feature_list_A, create_tail_chunk_list_trainingset, create_tail_chunk_list_A, filter_nonA_chunks_trainingset, create_gaf_list, create_gaf_list_A.

Examples

if (FALSE) { # \dontrun{

prepare_trainingset(
  nucleotide = "A",
  nanopolish = '/path/to/file',
  sequencing_summary = '/path/to/file',
  workspace = '/path/to/guppy/workspace',
  num_cores = 10,
  basecall_group = 'Basecall_1D_000',
  pass_only = TRUE)

} # }