ggDNAvis (version 0.3.2)

convert_modification_to_number_vector: Convert string-ified modification probabilities and locations to a single vector of probabilities (visualise_methylation() helper)

Description

Takes modification locations (indices along the read signifying bases at which modification probability was assessed) and modification probabilities (the probability of modification at each assessed location, as an integer from 0 to 255), as comma-separated strings (e.g. "1,5,25") produced from numerical vectors via vector_to_string(). Outputs a numerical vector of the modification probability for each base along the read. i.e. -2 for indices outside sequences, -1 for bases where modification was not assessed, and probability from 0-255 for bases where modification was assessed.

Usage

convert_modification_to_number_vector(
  modification_locations_str,
  modification_probabilities_str,
  max_length,
  sequence_length
)

Value

numeric vector. A vector of length max_length indicating the probability of methylation at each index along the read - 0 where methylation was not assessed, and probability from 0-255 where methylation was assessed.

Arguments

modification_locations_str

character. A comma-separated string representing a condensed numerical vector (e.g. "3,6,9,12", produced via vector_to_string()) of the indices along the read at which modification was assessed. Indexing starts at 1.

modification_probabilities_str

character. A comma-separated string representing a condensed numerical vector (e.g. "2,212,128,64", produced via vector_to_string()) of the probability of modification as an 8-bit (0-255) integer for each base where modification was assessed.

max_length

integer. How long the output vector should be.

sequence_length

integer. How long the sequence itself is. If smaller than max_length, the remaining spaces will be filled with -2s i.e. set to the background colour in visualise_methylation().

Examples

convert_modification_to_number_vector(
    modification_locations_str = "3,6,9,12",
    modification_probabilities = "100,200,50,150",
    max_length = 15,
    sequence_length = 13
)