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Extract tail features of a single RNA read from a multi-Fast5 file

Source: R/ninetails_core_functions.R
extract_tail_data.Rd

Extracts metadata and signal features of a single RNA read from a multi-Fast5 file basecalled by Guppy. The tail signal, as delimited by nanopolish polya function, is extracted, winsorized (to remove signal cliffs), and downsampled to 20% of its original length to facilitate further analysis. Pseudomoves are computed from the processed signal using filter_signal_by_threshold.

Usage

extract_tail_data(readname, polya_summary, workspace, basecall_group)

Arguments

readname

Character string. Name of the given read (UUID) within the analyzed dataset.

polya_summary

Data frame. The table containing data extracted from nanopolish and sequencing summary, as produced by extract_polya_data.

workspace

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

basecall_group

Character string. Name of the level in the Fast5 file hierarchy from which data should be extracted (e.g., "Basecall_1D_000").

Value

A named list containing per-read tail features:

fast5_filename

Character. Name of the source Fast5 file

tail_signal

Numeric vector. Winsorized and downsampled poly(A) tail signal

tail_moves

Numeric vector. Downsampled basecaller moves for the tail region

tail_pseudomoves

Numeric vector. Pseudomove states computed from the tail signal ({-1, 0, 1})

Always assign the returned list to a variable. Printing the full output to the console may crash your R session.

Details

The function performs the following operations:

  1. Reads raw signal from the multi-Fast5 file via rhdf5

  2. Retrieves basecaller moves and stride information

  3. Extracts the poly(A) tail region of the signal based on nanopolish coordinates

  4. Applies winsorization to the tail signal (winsorize_signal)

  5. Downsamples both signal and moves to 20% of original length via linear interpolation

  6. Computes pseudomoves using filter_signal_by_threshold

See also

extract_polya_data for preparing the polya_summary input, create_tail_feature_list for batch extraction, filter_signal_by_threshold for pseudomove computation

Examples

if (FALSE) { # \dontrun{

ninetails::extract_tail_data(
  readname = 'abc123de-fg45-6789-0987-6543hijk2109',
  polya_summary = polya_summary_table,
  workspace = '/path/to/folder/containing/multifast5s',
  basecall_group = 'Basecall_1D_000'
)

} # }