ggDNAvis (version 0.3.2)

convert_locations_to_MM_vector: Convert absolute index locations to MM tag (write_modified_fastq() helper)

Description

This function takes a vector of modified base locations as absolute indices (i.e. a 1 would mean the first base in the sequence has been assessed for modification; a 15 would mean the 15th base has), and converts it to a vector in the format of the SAM/BAM MM tags. The MM tag defines a particular target base (e.g. C for methylation), and then stores the number of skipped instances of that base between sites where modification was assessed. In practice, this often means counting the number of non-CpG Cs in between CpG Cs. In a GGC repeat, this should be a bunch of 0s as every C is in a CpG, but unique sequence will have many non-CpG Cs.

This function is reversed by convert_MM_vector_to_locations().

Usage

convert_locations_to_MM_vector(sequence, locations, target_base = "C")

Value

integer vector. A component of a SAM MM tag, representing the number of skipped target bases in between each assessed base.

Arguments

sequence

character. The DNA sequence about which the methylation information is being processed.

locations

integer vector. All of the base indices at which methylation/modification information was processed. Must all be instances of the target base.

target_base

character. The base type that has been assessed or skipped (defaults to "C").

Examples

convert_locations_to_MM_vector(
    "GGCGGCGGCGGC",
    locations = c(3, 6, 9, 12),
    target_base = "C"
)

convert_locations_to_MM_vector(
    "GGCGGCGGCGGC",
    locations = c(1, 4, 7, 10),
    target_base = "G"
)

convert_locations_to_MM_vector(
    "GGCGGCGGCGGC",
    locations = c(1, 2, 4, 5, 7, 8, 10, 11),
    target_base = "G"
)