Aggregates nanopolish polya quality control information.

Returns read counts for each qc_tag category (e.g. "PASS", "SUFFCLIP", "NOREGION", etc.), optionally stratified by a user-defined grouping variable.

Usage

nanopolish_qc(class_data, grouping_factor = NA)

Arguments

class_data

Data frame or tibble containing the raw class_data output from the ninetails pipeline (not the merged output).

grouping_factor

Character string (default NA). Variable used for grouping (e.g. "sample_name").

Value

A tibble with columns for the grouping variable (if provided), qc_tag, and n (the count).

Details

Caution: do not use the output of merge_nonA_tables as input, because that table is already filtered for quality. Use the raw class_data output from the ninetails pipeline instead.

Acknowledgements

This is the ninetails implementation of the get_nanopolish_processing_info function originally written by P. Krawczyk (smaegol) and incorporated in the NanoTail package: https://github.com/LRB-IIMCB/nanotail/blob/master/R/polya_stats.R. Variable names were adjusted to match the ninetails naming convention.

See also

read_class_single for loading class data, count_class for counting read classification labels.