Convert MM tag to absolute index locations (read_modified_fastq() helper)

This function takes a sequence, a SAM-style vector of number of potential target bases to skip in between each target base that was actually assessed, and a target base type (defaults to "C" as 5-methylcytosine is most common).

It identifies the indices/locations of all instances of the target base within the sequence, and then goes along the vector of these indices, skipping them if requested by skips.

For example, the sequence "GGCGGCGGCGGC" with target "C" and skips c(0, 0, 1) would identify that the indices where "C" occurs are c(3, 6, 9, 12). It would then take the first index, the second index, skip one, and take the fourth index i.e. return c(3, 6, 12). If instead the skips were given as c(0, 2) it would take the first index, skip two, and take the fourth index i.e. return c(3, 12). If the skips were given as c(1, 1) it would skip one, take the second index, skip one, and take the fourth index i.e. return c(6, 12).

The length of skips corresponds to the number of indices/locations that will be returned (i.e. the length of the returned locations vector).

Ideally the length of skips plus the sum of skips (i.e. the number returned plus the total number skipped) is the same or less than the number of possible locations. If it is the same, then the last possible location will be taken; if it is less then some number of possible locations at the end will be skipped.

Important: if the length of skips plus the sum of skips is greater than the number of possible locations (instances of the target base within the sequence), then the total number of taken or skipped locations will be greater than the number of available locations. In this case, the returned vector will contain NA after the available locations have run out. In the example above, skips = c(0, 0, 0, 0, 0) would return c(3, 6, 9, 12, NA), and skips = c(0, 2, 0) would return c(3, 12, NA).

Therefore, if the target base is totally absent from the sequence (e.g. target "A" in "GGCGGCGGCGGC"), then any non-zero length of skips will return the same length of NAs e.g. skips = c(0) would return NA, and skips = c(0, 1, 0) would return c(NA, NA, NA).

If skips has length zero, it will return numeric(0).

This function is reversed by convert_locations_to_MM_vector().

Usage

convert_MM_vector_to_locations(sequence, skips, target_base = "C")

Arguments

sequence

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

skips

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

target_base

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

Value

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

Examples

convert_MM_vector_to_locations(
    "GGCGGCGGCGGC",
    skips = c(0, 0, 0, 0),
    target_base = "C"
)
#> [1]  3  6  9 12

convert_MM_vector_to_locations(
    "GGCGGCGGCGGC",
    skips = c(1, 1, 1, 1),
    target_base = "G"
)
#> [1]  2  5  8 11

convert_MM_vector_to_locations(
    "GGCGGCGGCGGC",
    skips = c(0, 0, 2, 1, 0),
    target_base = "G"
)
#> [1]  1  2  7 10 11