ggDNAvis (version 0.3.2)

reverse_probabilities_if_needed: Reverse modification probabilities if needed (merge_methylation_with_metadata() helper)

Description

This function takes a vector of condensed modification probabilities (e.g. c("128,0,63,255", "3,78,1") and a vector of directions (which must all be either "forward" or "reverse", not case-sensitive), and returns a vector of condensed modification probabilities where those that were originally forward are unchanged, and those that were originally reverse are flipped to now be forward.

Called by merge_methylation_with_metadata() to create a forward dataset, alongside reverse_sequence_if_needed(), reverse_quality_if_needed(), and reverse_locations_if_needed().

Usage

reverse_probabilities_if_needed(probabilities_vector, direction_vector)

Value

character vector. A vector of all forward versions of the input probabilities vector.

Arguments

probabilities_vector

character vector. The probabilities to be reversed for each sequence/read. Each read should have one character value, representing a comma-separated list of the modification probabilities for each assessed base along the read e.g. "230,7,64,145". In most situations these will be 8-bit integers from 0 to 255, but this function will work on any comma-separated values.

These comma-separated characters/strings can be produced from numeric vectors via vector_to_string() and converted back to vectors via string_to_vector().

direction_vector

character vector. Whether each sequence is forward or reverse. Must contain only "forward" and "reverse", but is not case sensitive. Must be the same length as probabilities_vector.

Examples

reverse_probabilities_if_needed(
    probabilities_vector = c("100,200,50", "100,200,50"),
    direction_vector = c("forward", "reverse")
)