makeAverage1merSub: Make a 1-mer substitution model by averaging over a 5-mer...

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Make a 1-mer substitution model by averaging over a 5-mer substitution model

Description

makeAverage1merSub averages substitution rates in a 5-mer substitution model to derive a 1-mer substitution model.

Usage

makeAverage1merSub(sub5mer)

Arguments

sub5mer

a 4x1024 matrix such as that returned by createSubstitutionMatrix and that returned by makeDegenerate5merSub with extended=FALSE. Column names should correspond to 5-mers containing the central 1-mer to mutate from. Row names should correspond to nucleotides to mutate into. Nucleotides should include "A", "T", "G", and "C" (case-insensitive).

Details

For example, the substitution rate from "A" to "T" in the resultant 1-mer model is derived by averaging the substitution rates into a "T" of all the 5-mers that have an "A" as their central 1-mer.

Value

A 4x4 matrix with row names representing nucleotides to mutate from and column names representing nucleotides to mutate into. Rates are normalized by row.

See Also

See makeDegenerate5merSub for making a degenerate 5-mer substitution model based on a 1-mer substitution model.

Examples

# Make a degenerate 5-mer model (4x1024) based on HKL_S1F (4x4)
degenerate5merSub <- makeDegenerate5merSub(sub1mer = HKL_S1F)

# Now make a 1-mer model by averaging over the degenerate 5-mer model
# Expected to get back HKL_S1F
makeAverage1merSub(sub5mer = degenerate5merSub)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.