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Substitute short zero-gaps surrounded by nonzero pseudomoves

Source: R/ninetails_misc_helper_functions.R
substitute_gaps.Rd

Smooths the pseudomove vector by filling in isolated zero-gaps (length < 2) flanked by identical nonzero values. This avoids redundancy introduced by the z-score thresholding algorithm when the signal is jagged, so a single modification region is reported instead of multiple fragmented segments.

Usage

substitute_gaps(pseudomoves)

Arguments

pseudomoves

Numeric vector. Pseudomove vector produced by the z-score filtering algorithm (filter_signal_by_threshold), corresponding to the tail region of the read of interest as delimited by nanopolish polya function.

Value

Numeric vector. Adjusted pseudomoves with short gaps filled.

See also

filter_signal_by_threshold where this function is called as a post-processing step

Examples

if (FALSE) { # \dontrun{

substitute_gaps(pseudomoves = pseudomoves_vector)

} # }