convert_locations_to_MM_vector: Convert absolute index locations to MM tag...

In ggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

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")

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").

Value

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

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"
)

ggDNAvis documentation built on Nov. 5, 2025, 7:36 p.m.