Counts reads by number of non-A occurrence instances.

Categorises reads into three abundance bins based on how many separate non-A residue occurrences (instances) were detected per read: "single" (1), "two" (2), or "more" (>= 3). Returns the count of reads in each bin, optionally stratified by a grouping variable.

Usage

count_nonA_abundance(residue_data, grouping_factor = NA)

Arguments

residue_data

Data frame or tibble containing non-A residue predictions from the ninetails pipeline.

grouping_factor

Character string (default NA). Name of a column to use as a grouping variable (e.g. "sample_name").

Value

A tibble with columns for the grouping variable (if provided), instances (one of "single", "two", "more"), and count (the number of reads in each bin).

See also

count_residues for counting total residue hits, count_class for counting read-level classes, read_residue_single for loading residue data.

Examples

if (FALSE) { # \dontrun{

nonA_abundance <- ninetails::count_nonA_abundance(
  residue_data = residue_data,
  grouping_factor = "sample_name")

} # }